The Ikari Identity
by AngelNo13Bardiel
Summary: <html><head></head>Shinji Ikari awakens with time lost and finds his world turned even more sideways... -Story completed/C&C appreciated-</html>
1. Blues from a Gun

**DISCLAIMER:** I still don't own Evangelion or any of the characters, they're still property of…well, whoever owns them these days. This fic's got nothing to do with Rebuild, just the original series/movies. Timeline places this sometime after the 16th Angel, but before episode 24. It also borrows a fair amount of ideas/scenarios from the Bourne franchise, just so you know. And lastly, 'this' is thoughts and "this" is speech.

**THE IKARI IDENTITY**

Chapter 1: Blues from a Gun

* * *

><p>'Another damned rainy night,' the old captain thought grimly. The rain had been hard for several nights now with no sign of letting up soon. Sighing, the man took out a cigarette from a pack. He was about to light it when a strange sight in the water stopped him. 'What the hell…' he thought, reaching for the binoculars around his neck. A look through them confirmed what he thought: a body was floating about in this miserable weather. "Hey!" the captain shouted to the crew. "Get your asses out here! We've got a floater!"<p>

After steering the boat around to the body, a couple of the fishermen threw a net overboard and picked it up onto the deck. The captain looked over it, a boy not older than fourteen or fifteen. He was dressed in a form-fitting full-body black suit that covered up to his neck. Then he noticed the slow rise and fall of the young man's chest. "Holy…" he said with a start, "he ain't dead yet." He then motioned for the two men who'd pulled the boy from the water to get him below deck and into the makeshift infirmary onboard.

Upon getting him down there, the ship's doctor examined the boy. On his back were two small wounds, apparently gunshots. Cutting away the plastic-like fabric of the suit, he proceeded to administer anesthesia to the young man and remove the bullets. One had struck him in the lower part of the left shoulder, nothing more than a flesh wound with a round inside. 'Easy enough to pry out,' he thought as he used a pair of pliers to do the job. The other, however, struck him in the shoulder blade, a few inches from the spine. Pulling out the round, the doctor discovered that the second round had struck something within the boy's skin. Cutting a little deeper, he found a strange microchip attached to the muscle near the backbone. The round had nearly missed it, only barely catching the edge. Cutting away the small wires attaching it to the muscle, he looked at the device carefully, not having a clue what he was seeing. His gaze lowered down to the boy, he mused, "Now what the hell do you make of that?"

* * *

><p>Shinji Ikari's eyes snapped open, his body sitting bolt upright. Immediately, he regretted this action as a wave of pain coming from his back made him fall right back onto the small bed he occupied. Gritting his teeth to block some of the pain, he looked about the room. 'Where…where am I?' he thought. It certainly wasn't his room or the NERV infirmary, that much was certain.<p>

"Ah, glad to see you've come to," an unfamiliar voice came from across the room. At the sound, Shinji nearly jumped out of bed, the motion sending another ache through his person. "Sorry 'bout that, didn't mean to scare you half-to-death," the voice continued. Casting his gaze towards the sound, the boy was met with the sight of a middle-aged man dressed for cold weather.

"W…who are you? Where am I?" Shinji asked, eyes wide.

The captain sat down in a wooden chair close to the door and sized up the young man his crew had pulled out of the sea. "Name's Mathieu," the man started. "and you're on my ship. Damned lucky we saw you, y'know?" As Shinji tried to sit up again, the captain noticed the pain in his expression. "Hey…take it easy for a bit," he started, lighting a cigarette. "Not everyone lives from gunshot wounds, y'know?"

Shinji's expression dropped further, his eyes remaining wide. "G-gunshot?" he asked.

"Yep," Mathieu answered. "Two of 'em, probably a .22 by the size." The quiet in the room lasted for a minute before the man decided he needed at least a few answers from his guest. "So…what's your name?"

Shinji winced again as he sat up and thought over his answer. "S…Shinji, sir," he said.

"Shinji, eh?" Mathieu asked, getting up from the chair and walking over to a cabinet on the other side of the room. "Well, I'll say this," he said, pulling out a bag and placing it in front of the boy. "There's some strange things you came onboard with…"

Looking into the bag, Shinji saw a couple of items that puzzled him. One looked to be a plug suit, black-colored and cut into two. The other was a dented and fried computer chip with some blood on it.

"Not even sure where to begin with either one, to be honest," Mathieu said. "How 'bout you?"

Shinji shook his head. The plug suit looked to be the same as the one he wore for tests and battle…but it was missing the neural connectors and the life-support device on the arm. The top half showed two small holes near the left shoulder on the back, the same place as the pain he was feeling. The chip, on the other hand, he had absolutely no idea about. "Never seen either before," he said. "This…came out of me?" he asked, holding the chip.

"Yeah," Mathieu said. "If I had to hazard a guess, I'd say it was a GPS tag."

'Something NERV probably did,' Shinji thought with a sigh, shaking his head. "Where'd you say you pulled me from?" he asked.

"A couple-dozen miles from the Tokyo-2 shoreline," Mathieu answered. "Dunno how long you were adrift, though."

Laying back down, Shinji felt at a loss for what he'd been told. 'Shot and adrift at sea…' he thought. 'What the hell was I doing out there?'

"Me and the guys are glad you came around," Mathieu said after a long silence. "Been worrying you wouldn't pull through…"

Shinji's gaze fixed back on the older man. "Wha-" he started, "how long have I been here?"

Mathieu tried as best as he could to hide his expression from the boy. "Almost five weeks…"

Shinji's eyes widened as much as they could. 'Five weeks…' he thought. 'Misato must think I'm dead or something,' he mused, feeling sorry for what he'd probably put her through.

"So where're you from?" Mathieu asked. "I can already tell you're from this country, at least…"

Shinji closed his eyes and sighed. "Tokyo-3," he said after a moment.

Standing up, Mathieu walked over to the boy and put a hand on his unhurt shoulder. "Ah, that's good then," he said, "we'll be pulling into Tokyo-2 in a week or so. Not too long a walk to home from there, huh?"

Shinji shook his head. "No sir…" he said quietly as the captain headed for the door.

Just before he exited, Mathieu turned back to the young man. "I get the feelin' you're not tellin' me everything. But I understand, man's gotta have some secrets, right?"

With the captain having left the room, Shinji stared at the ceiling for quite some time in silence. His life had been turned in some rather dark directions lately…but whatever had happened to him he couldn't even fathom. 'Everything's just as skewed as after the last few Angels,' he thought bitterly. 'But what in the world was I doing out there?' Sighing heavily, he pulled the sheet on the bed up and tried to shut out the pain in his back. 'At least it's a pain I'm used to…'

* * *

><p>Eight days later, the ship pulled into the harbor at Tokyo-2. Waking up that morning, Shinji put on a t-shirt and pants one of the shorter crew members had donated to him along with a pair of shoes. 'A little big, but they'll do,' he thought. The pain that had been with him since he awoke on the boat had subsided a bit, making him able to get around with no problem. Leaving the makeshift infirmary and getting out onto the deck, the boy was met by the captain.<p>

"Well lad," Mathieu said, holding a hand outstretched. "I suppose this is where we part company, eh?"

Smiling as best as he could at the man, Shinji accepted the handshake. "Uh…sure. Thanks for everything, sir," he said. "I only hope I wasn't a burden…"

"Nonsense!" Mathieu insisted, shaking his head. "Always feels good to help someone in need," he finished, handing the boy a raincoat. "Consider it a final parting gift. Rain'll be coming back soon."

Nodding to the older man, Shinji accepted the garment and put it on. "Hope to see you again one day," he said, walking towards the landing plank.

"Of course," the captain agreed. "It's a wide world out there, and you just never know…"

With a final wave, Shinji stepped out onto the docks of Tokyo-2. The smell of salt was strong in the air, the city certainly seeming more alive than Tokyo-3 'Not really a surprise considering…' he mused, walking out into the city. 'Most of the city's population had come here after what happened to Unit-00 because of that last Angel,' his thoughts continued, feeling the sadness come up again.

Several hard rain drops shook the thoughts from his mind momentarily. Pulling the hood over his head and resuming his walk, Shinji soon came upon a bank of payphones. 'Might as well try,' he thought, pulling a few coins out of his pocket and putting them in one of the machines. As the rain started to pick up, he dialed the number for Misato's apartment. Several rings later, the familiar answering machine picked up. Sighing, he hung the phone up and leaned against a wall nearby. 'Great…looks like I'm walking,' he thought with a hint of sarcasm.

* * *

><p>After a few hours worth of walking, Shinji had begun to notice things he hadn't before. For one, he was avoiding people more than he usually did. 'Not that that's a whole lot,' he had thought once or twice. But it seemed like more like instinct to him now, not the deliberate avoidance he'd done so often. The further he got into town, the more he was heading off the beaten path and into the side streets and alleys. And for the life of him, he couldn't understand it.<p>

Another had been the way he was sizing up people who had been curious. 'Dunno what the hell that was all about,' Shinji mused. The funny thing was, he felt confident none of them could take him in a fight. And that thought had felt like a gut-punch. He'd been in very few real fights in his life, Angels battles notwithstanding, and none of those he'd won…so he had no clue where these odd trains-of-thought were coming from.

"What's going on with my mind?" Shinji asked quietly, standing in a dark alley with the rain pouring down on him. Looking around, he saw a newspaper machine. Curious to know exactly how long he'd been 'lost', he walked over to the machine and saw the date. 'It's like he said, just over six weeks…' he thought, eyes wide and not having the slightest idea what had transpired. 'Maybe a battle went badly?' me thought, resuming his walk out of the city limits. 'No, Angels wouldn't use human weapons.'

And that was a main thought that'd been with Shinji since he awoke over a week ago: who in the world would've tried to kill him? NERV wasn't really under fire from anyone, as best as he could tell. Hell, they were saving mankind from the Angels. "So…why me?" he thought aloud. He'd also wondered about Asuka and Rei, if any attempt had been made on their lives. 'God, I hope not,' he thought. Although recent events had (for lack of a better word) soured things between everyone, he still didn't want to imagine his friends hurt or worse. 'Not that things could get a whole lot worse,' he thought with a heavy heart.

* * *

><p>After leaving the city limits of Tokyo-2, Shinji spent the next day-and-a-half in the forests between there and Tokyo-3. Partially for natural cover, partially to avoid anybody else. "Guess that time camping with Kensuke taught me something," he said while seated at the foot of a large tree. "Should really thank him for that one of these days…"<p>

Night had fallen, and Shinji had built a fire nearby the tree's base with whatever dry wood he had found. It provided some heat, but he was still quite cold. 'Feels like summer every day,' he thought, 'but nights can get pretty chilly. At least it stopped raining.' And while that was some solace, the moisture and chill in the air had done their best to keep the heat out of the boy.

Facing the fire and pulling the raincoat around him, Shinji prepared himself for what was sure to be another fitful night's sleep. "Haven't been sleeping well since I came to, actually," he mused aloud. That much was certainly true, the nights since then had been restless for him. The dreams were fractured, not really making much of any sense, and they'd be gone not long after waking. But deep down, he knew they were about whatever had happened to him…

* * *

><p>Several miles from Shinji's nightly stop, a phone rang in a large office.<p>

"Yes?" a man's voice answered.

The voice on the other end talked for a half-minute before falling silent.

"I see…continue keeping watch," the voice spoke again. Returning the phone to its cradle, it spoke up again to another in the room. "The Third Child was spotted in Tokyo-2 two days ago."

"Is that where I should go?" a soft feminine voice asked.

"No," the man's voice answered. "We know where he'll be going. Head there and give him his…homecoming."

"Understood," the female voice said. Several seconds of footsteps echoed through the large office before the sound of a door opening and closing is heard.

"Is it wise to send only her?" another voice asked.

"Have faith," the man's voice replied, the smirk nearly audible. "She'll take care of it."

* * *

><p>The following evening, Shinji made it back to the outskirts of Tokyo-3. Looking out over the lake created by Unit-00's destruction, he felt the same heavy sadness come over him. Shaking his head of the thoughts, he mused, 'No time for that right now. I need to get back to Misato's.'<p>

As he had done in Tokyo-2, Shinji took the most out-of-the-way path back there. 'Like my mind's telling me to avoid being seen,' he thought, 'although there can't be many people left that could see me.' Crossing several quiet streets and back-alleys, he walked up to the familiar building he lived in with Misato and Asuka. 'Well, and Pen-Pen,' he thought, remembering his guardian's pet, 'but she sent him to Tokyo-2 with Hikari.'

The building was one of the few that had been undamaged after the last few Angel attacks, something Shinji hadn't been grateful for until right then. 'It'll just be nice to be in a familiar hiding place,' he thought with a hint of humor. After riding the elevator, he approached the door to the apartment. 'I hope someone's home, I don't have a key,' he thought, mentally kicking himself for such an oversight. Stepping up to the door, his eyes went a little wide as he noticed the lock had been broken. Hand shaking, he reached out and slid the door open.

Walking into the dark of the hallway, Shinji could see that the living room had been ransacked. Moving about the apartment, he discovered the same had been done to the kitchen and two of the bedrooms. His room, oddly, had been spared. 'Probably nothing to find here,' he thought, remembering how little he owned. But his clothes, cello, and S-DAT player were missing…that was certainly strange. None but the cello were worth much, but it didn't look like they were stolen. Removing the raincoat, he closed the door to his room.

Returning to the living room, Shinji began to pace the small area. Possible scenarios played out in his head, not many of them very good. "Was there an evacuation?" he asked in the darkness, finally stopping his pacing. "D-did whoever tried to kill me get to them?" A soft click behind him shook the thoughts from his head.

"Shinji Ikari?" a man's voice asked.

Turning around, Shinji caught sight of a couple of Section Two agents. Neither one of them could've been older than twenty-one. And one of them was pointing a silenced handgun at the him. He nodded at them and spoke up. "W-what's this? Where's Major Katsuragi?" he asked, trying to hide the waver in his tone.

"We are unaware of the major's whereabouts at this time," the agent pointing his gun at Shinji answered. "Enough questions…we've been ordered to bring you back alive and…mostly unharmed."

"What? On whose orders?" Shinji asked, fear becoming a knot in his gut.

"Commander Ikari," the other agent replied.

"Father…" Shinji seethed under his breath, gritting his teeth and clenching his fists.

Upon Shinji's reaction, the agent with the gun spoke up. "Come on, you've got an appointment with the Commander."

The other agent walked behind the Third Child. As he began to put a pair of handcuffs on Shinji, the boy felt a strange instinctual urge course through him. In one swift motion, he quickly removed the cuffs from the agent and linked them on the man's wrists. And then made his point with a hard kick to the agent's chest, sending him sprawling across the floor.

As the other man began to react, Shinji made a grab for the man's arm. Two silenced shots came out, the barrel pointed down at the wood floor. The boy twisted the arm around and gave it a few sharp strikes, the handgun becoming lost from the agent's grip and onto the floor. The young man then used the leverage to bring a forearm down on the back of the agent's neck. He slumped to the living room floor, the fight having left him for now.

By now, the other agent had regained his footing and pulled his own gun. Shinji's attention quickly snapped back to him, diving behind the couch to avoid the shots. Counting off fifteen like it was ingrained, he quickly lunged out and for the gun he'd disarmed the other agent of. Taking quick aim, the Third Child shot the agent in both kneecaps and the arm holding the gun.

The agent fell to the ground in a heap, pain evident across his face. Rising from the floor and walking over to the man, Shinji kicked his gun down the hall. Stepping closer, he pointed the weapon at the agent's head. But as he was about to squeeze the trigger, his expression dropped upon realizing just what he'd done…the skills he'd just utilized. Skills he was certain he didn't have.

Shinji stood there, looking at his hands and the gun in one of them. Shaking and breathing heavily, he dropped the weapon and walked with unsteady footing towards the apartment's front door. 'Wh-what the hell did I just do?' he thought, a rush of adrenaline still surging through his frame. His thinking was cut off by a quick foot to his chin by an unseen third party. Upon regaining his senses, he looked at the person who has attacked him…any anger in his expression changed instantly to a mixture of shock and surprise upon seeing who it had been.

Standing over him was Rei Ayanami, the enigmatic First Child. She was clad in the same black plug suit he'd been wearing when Mathieu's ship had rescued him. And armed identically as the other two agents he had just dispatched. "Ikari," she spoke softly, the gun in her hand never wavering an inch as it was pointed at his face, "the Commander has need of you. Come along quietly…he said you were to be brought back alive. But if you persist, you will not be unharmed." Then, as if to make her point, she removed the gun's safety with a sharp click…

*******To be continued…*******

**A/N:** Okay then…one down, a few more to go. I figured it was time for something different (at least a little bit, for now) from me. And the idea had been with me for a month or so, so I figured it was time for another.

Who knows? Might keep this pace up and polish off a few more after this…

And, as promised last time…

*******Omake time!*******

We find the author seated at his computer, typing away at the last bit of this chapter.

Bard: Well…that's the first part down. (looking up at the room's newest occupant) Ah, so glad to see you all again!

Upon hearing those words, Mitsumi floats into the room and hugs the camera.

Mitsumi: (beaming) YAY! It's so nice to have you all back!

Bard: Ah…Mitsumi…

Realizing she'd been a little too glad to see the audience again, Mitsumi releases the camera and blushes slightly.

Mitsumi: (nervously) Oh, sorry about that. It's just that we haven't seen them in so long!

Bard: (sighing) I know, I know…

Mitsumi: (smirking) 'Bout time you got back to work, y'know?

Bard: (sweatdropping): Alright, I get it already!

Mitsumi: Oh, I just remembered something… (puts on her best mean look) I saw what you did in that other new one. You told me you weren't gonna do anything ecchi!

Bard: (sweating bullets) Ah…that. Well, at least I didn't get any more descriptive than-

Mitsumi: (cutting him off) THAT'S NOT THE POINT!

Bard: (incredulous) It isn't? I think it ended at being more "cute" than "hawt", agreed?

Mitsumi: (thinks it over for a moment) Okay…I'll give you that one. (a dreamy look comes over her face) It WAS really precious…

Bard: (smiling) Indeed, it was the proudest moment I've had being a fan of them.

Mitsumi: Really?

Bard: Yep.

Mitsumi: (trying her best Asuka impression) Then I guess I'll allow it…but nothing more than that. You even think about writing a le-

Bard: (cutting in) The thought never even crossed my mind.

Mitsumi: (rolling her eyes and floating out of the room) Baka author…

Bard: (sighs and slumps in his chair, then looks at the camera) Well, that doesn't mean I can't get to that level again, right?

Mitsumi: (from the other room) I HEARD THAT!

*******End Omake*******

Pre-read for this chapter was done by the team of Dark Machine, Eric Blair, gesser87, and JimmyWolk. Thanks, guys.

Small note: this chapter and all previous/following it were written around late June/early July last year. So a quick "sorry" to everyone who may have been waiting for something after TLaWR. Revisions and pre-reading can take quite a bit of time, it would seem…

For any of you who are new to the community, all of my older (2004-2006) works have undergone a small bit of tweaking (as of the 14th of June 2010). So go take a look, tell me what you think. And review! Even if it's not positive, review!

As usual: good comments will be appreciated, bad ones will be ignored (or kept for firewood). But I do favor good/helpful criticism, so send it my way!

**-AngelNo13Bardiel-**


	2. Truth Hits Everybody

See Chapter 1 for disclaimer.

**THE IKARI IDENTITY**

Chapter 2: Truth Hits Everybody

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><p>From a rooftop nearby, another party watched the current scene in Misato's apartment playing out. "Shit!" a female voice said, looking through binoculars. "Finally shows up only to nearly get himself killed!" Sighing heavily, she prepared to go right into the lion's den. "Son of a bitch, that idiot had best appreciate this…"<p>

* * *

><p>Back in the apartment, Shinji was still laying down trying to wrap his head around what had just happened. He had just disarmed and nearly killed two Section Two agents sent to bring him back to the Commander, but it felt like he had seen someone else do it, using his body; memories and reflexes and reaction that weren't his own, using skills he was unaware even existed; he had moved so fast, so precise, with movements focused and intended to deliver as much disabling pain as possible in as…little time as he could.<p>

Then there was Rei Ayanami standing over him, with a gun in her hand pointed at him, and Misato's apartment seemed to have become a war zone; taken apart, furniture and appliances strewn around the floor. And still, there was no trace of Misato or Asuka.

"Rei," Shinji spoke up, his voice cracking. "W-what the hell is going on?"

"I told you," Rei spoke in her usual chilly tone, "Commander Ikari has had people looking for you for weeks. You are still needed at NERV. Your whereabouts during that time can be explained another day." Pointing the gun towards the Third Child's head, she continued. "Now get up. I do not wish to harm you greatly."

As he stood up, Shinji felt his instinct take over and decided to even the odds a bit. Lunging for the gun, he knocked it loose from the First Child's hand and tried to hold her in an armlock. "Stop this, Rei," he spoke with a voice as cold as his father's. "I won't fight you."

"Then you will force me to hurt you," Rei replied. Breaking his grip, she gave him a hard right jab to the stomach. Pushing the advantage further while he was winded, she delivered a short kick to his left side.

Shinji grunted, pulling himself off the floor quickly. As Rei came at him with another kick, he caught her leg with his crossed wrists. "Enough!" he shouted, intent on stopping her unprovoked assault.

Rei said nothing, trying to free herself from his grip. Using her light weight, she backflipped and caught Shinji in the jaw with her other foot, freeing the caught leg before landing with a soundless grace.

Shinji, meanwhile, found himself on the floor again. 'This really isn't working,' he thought. Rei was certainly more serious about this than he was, even with the unknown-to-him skills he was using. All he was doing was fending off her strikes, she seemed to be ready to crush what little spine he had.

The sound of glass breaking took the attention of both of the room's conscious occupants. As the patio door practically exploded inward, a shape came through and hit Rei, knocking her back a few feet. As Shinji regained his footing, his gaze was caught by the room's newest occupant. A feminine form with a familiar red mane told him all he needed to know. "Asuka…" he thought aloud.

Asuka Langley Sohryu stood before him, wearing a dark beige sweater and blue jeans. The shoes she wore he hadn't seen since when she moved in, a black pair built in a heel-boot hybrid style. Oddly, Shinji noticed, her hair did not contain her neural connectors. 'Rarely seen her without them, now that I think about it,' he thought.

"You okay?" Asuka asked, breaking his train of thought.

Feeling more out-of-the-loop than ever, Shinji could do nothing but stand up and nod.

Shaking her head angrily, Asuka shot him her best mad look. "Idiot! Take this more seriously!" she berated. "She could've easily killed you…"

Rei groaned and got to her feet, the mildest look of anger on her face. "Pilot Sohryu," she spoke softly.

Asuka turned her attention back to the other girl. "Hello again, First," she said, the last word practically drenched in venom. "Get behind me," she whispered to Shinji, "this is gonna get ugly."

Nodding, Shinji edged backwards and well away from both of his fellow pilots. 'I knew there was some hard feelings…but what the hell is this?' he thought of the scene before him.

"You would stop me?" Rei asked, her eyes never leaving the redhead.

"I'd be happy to," Asuka answered, cracking her knuckles.

"My orders say nothing of sparing your life," Rei warned.

"Never dreamed they would have," Asuka spat back.

Deciding that the time for words was over, Rei made the first move. A hard left followed by a wide kick, both easily evaded by Asuka. The redhead struck back with a leg sweep that took the First Child off her feet…for just a second. Springing back onto her feet, the pale girl found herself fending off the Second Child's furious blows while looking for an opening. Seeing a chance, she evaded one of the punches and used the redhead's momentum to shove her into the wall near the kitchen.

Dazed from that, Asuka shook her head and glared hard at the other girl. The attack hadn't done any damage, but it did hurt like hell. "Bitch…" she fumed under her breath. Just as Rei attempted another kick, the redhead ducked it and brought out a roundhouse of her own. The First Child caught it easily, but was caught unaware as the other leg was swung around and into her face. Both girls ended up on the floor, only with the redhead keeping her footing.

From across the room, Shinji could only watch the spectacle before him with a strange expression. It was a graceful ballet of violence like nothing he'd seen before. 'And I'd bet Kensuke would pay greatly to see it happen,' he had thought off-hand, the whole thing seeming surreal.

Sprawled out on the living room, Rei picked the gun she'd been carrying back up and brought it around to the others. Just as it drew a bead on her, Asuka kicked the gun high up above the two of them before reaching for it. Her hand finding a grip on the weapon, she brought it down to the winded First Child's form. "Don't even fucking move," she threatened, trying to catch her own breath, "or swear I'll do it."

Shinji's eyes widened at what was going to unfold. He quickly closed the distance and pulled the gun up from Rei's head. "No, Asuka!" he shouted. "No killing."

"And why the hell not?" Asuka seethed, not understanding what he was doing.

"She's still our friend…" Shinji said quietly. "Regardless of what just happened." Rei's gaze moved around to him, her expression one of slight surprise.

Asuka continued to give him an angry stare, but relented. "Fine," she said. "But it's on your head!" She then emphasized this by bringing up a boot-covered foot and knocking the First Child out.

"Asuka!" Shinji yelled.

"Hey, she's not dead…" Asuka stated in a cold voice. Looking out of the window, her expression instantly became much more serious. "Shit! Here they come…" Running towards the door, she grabbed up Shinji's collar and pulled him forcefully out of the apartment.

"Wha-" Shinji managed after some work. "Who's coming?"

"Section Two agents," Asuka said, releasing him and walking over towards the stairs. "Things are gonna get a lot more complicated from here." Readying the gun, she opened the door to catch sight of one of the agents. Making a mad dash for him, she took a shot at his arm before tackling the man hard, which knocked him out. "See? I can show some restraint," she said to Shinji in her best haughty voice.

"This really isn't the best time," Shinji said, looking down into the stairwell.

"Don't bother," Asuka said. "We're not going that way."

"Huh? Where else is there?" Shinji asked.

"Up, of course!" Asuka said, her tone even and controlled. "Gotta evade them somehow…"

Walking up several flights of stairs, the two pilots found themselves on the building's roof. Looking down at the two Section Two vehicles pulling up, Shinji began to feel a great unease. "Are you sure about this?" he asked.

"Not much choice," Asuka replied. "Not unless you'd like to go with them." Walking over to one side of the building, she pulled two pairs of gloves from her pocket and handed one pair to the boy. "I think you'll want these for what's coming," she said, putting on a pair herself.

Not understanding, Shinji looked over the side of the building to see what she meant. Attached to the roof and leading down into an alley was a rope. "Wait a minute," he began, "you don't mean-"

"Oh yeah," Asuka explained, "that's exactly what I mean. Don't think too much about it. Just grab on and slide down. That's what the gloves are for." Hefting her weight over the side of the building, she began the trip down to ground level.

Shinji could only watch as his roommate slid down the rope and onto the street. Sighing heavily, he did just as she had and felt a fearful rush as the ground approached fast. Once on the ground, he shook his head at what had just happened. "And I thought I'd been through everything…" he mused. Walking over to where Asuka stood, he kept watch for anyone coming their way. "Okay, what now?" he asked.

"Just follow me," Asuka answered. "Stay low and stay quiet."

Shinji nodded and followed her lead down the alley and out onto another quiet street. After a short walk into a side-street, the two came upon a black Renault Alpine parked in the recess. "Hey, this looks like…" he said.

"That's because it is," Asuka cut in. "She's just been given a paint job." Realizing something she'd forgotten, her mood became deadly serious. "Hey, come here for a second."

Shinji walked over to her, her change in mood increasing his unease. That was only amplified as she quickly turned him around and pulled his shirt up. "Wh…what the hell?" he asked, hearing a click behind him.

Asuka looked over his back, the two healing gunshot wounds sewn up. Staring hard at the lower one, she whirled the boy around to face her. "Alright, where is it?" she asked him, a pocket knife in hand and a deathly glare on her face.

"I don't know what you're talking about!" Shinji raised his voice slightly. The knife was nearly at his neck.

Shoving him up against the nearby wall, Asuka continued to stare daggers at him. "Don't even fuck around with me right now!" she demanded. "Where's your chip?"

Shinji's eyed widened at the question. 'How could she know about that?' he thought. "I was shot…one of the rounds hit it," he explained, hoping to redirect her anger. With that, Asuka released him and put the blade away. "It was GPS, wasn't it?" he asked, feeling glad to be in one piece.

"No," Asuka said in a low voice, "much worse." Opening the door to the car, she motioned for him to get in. "It's something that just needed taking care of," she said quietly. "Now come on, we're getting out of here."

Seating himself in the passenger side, a thought occurred to Shinji. "Asuka," he said, "can you even drive? I mean, you're only-"

"Now is not the time to be bringing that up," Asuka threatened him. "Let's just say we've both got some serious new skills…"

Shinji decided right then to shut up and buckle up. Turning the key, Asuka started the car up and slowly eased it out of the narrow alley. 'Hope there's no one around,' she thought as she turned out onto the street. For a couple of blocks, it was all quiet. That is, until a left turn nearly ran them into a Section Two SUV. A few handgun rounds were shot in their direction, one of them shattering the back window. "Shit!" she yelled, shifting wildly and pushing the gas as hard as she could. "So much for the easy way," she continued while giving the wheel a hard turn.

The sports car managed to keep ahead of the larger vehicle, Asuka trying desperately to lose the tail. After several more blocks, she began to form an idea. "Shinji," she said to her passenger. "Backseat floorboard, behind you."

Unbuckling himself, Shinji climbed back and looked for what she'd requested. And there he found it, a submachine gun. "This what you meant?" he shouted over the engine's roar.

"Don't just sit there!" Asuka yelled back, making the car take another hard right. "Take care of it!"

Nodding, Shinji edged himself partly out of the window and aimed at the SUV's front grill. That same feeling in the apartment took control as he looked for the right spot. Giving the trigger a small squeeze, a short burst erupted from the weapon and struck the engine block dead-on. 'Not going anywhere now,' he thought as he pulled himself back inside the car, feeling disconnected from the whole event.

Asuka was trying her best to keep control of the car, heading back to one of the exits from town. As she neared the street she was seeking, another SUV blocked her off. "Goddamn it!" she fumed, having had more than her fill of this situation. "I swear to all that's holy, I'm not driving next time!" Making a quick 180-degree turn, the redhead put as much weight into the gas pedal as she could.

Shinji pumped out a couple more bursts in the direction of the vehicle following them. One hit the front left tire, causing the SUV to swerve wildly but still keep chase. As he readied to fire another burst, a click told him he'd run the weapon dry. "Oh, for the love of…" he said angrily, tossing the empty gun into the backseat. "I'm out, you'll have to take care of this one!"

"Just like always…" Asuka said under her breath, sighing. Making another hard turn, the Second Child steered the car a few streets over…and around the lake made by Unit-00's destruction. The flat front tire on the SUV following them made it nearly impossible for the driver to keep control.

Looking in the rearview mirror, Shinji saw the larger vehicle hit the water running. 'And that makes two…' he thought, realizing that was the only two that had been outside the apartment building. Exhaling sharply, he noticed they were leaving the city limits and out onto a road leading into Japan's countryside. "I think I've had enough of this for several lifetimes…" he thought aloud.

"What?" Asuka asked.

"Nothing…" Shinji replied, the enormity of the night's happenings setting heavily on him. Looking over the redheaded driver, he afforded himself a small smile.

Noticing the boy's stare, Asuka spoke up. "What're you staring at?"

Shaking his head, Shinji continued to smile. "I just realized…you drive like Misato."

"Oh really?" Asuka said with a smirk. She then gave the wheel a hard jerk to the right and left, tossing the boy about the front seat. "Still think it's so funny?" she asked, the slow simmer of rage in her tone.

Shinji said nothing, only buckling himself back into the seat and watching out the window.

* * *

><p>Miles away, a call was being taken in a large office.<p>

"I see…" a man's voice said. "That is most…unfortunate." Placing the phone back in the cradle, Gendo Ikari's expression didn't even betray a hint of worry. For him, all was going to plan.

"It was the Second, wasn't it?" another voice asked from across the room.

"It is of no consequence," the Commander said. "She will be dealt with in due time."

"I told you to send me along with the First," the voice said.

"No, you are my protection in her stead," the Commander said. "The Second and Third will be no threat soon enough…"

"So she is still alive?" the voice asked.

"Indeed," the Commander answered. "It seems he isn't willing to hurt Rei."

"That could be used to your advantage," the voice spoke.

"Yes, but I will not have her take unnecessary risks," the Commander replied. "Now that she is truly…irreplaceable. She is still needed for the scenario."

"Ah yes, of course," the voice agreed. "Then all proceeds as planned…"

* * *

><p>Nearly an hour into their drive, Shinji decided to stop pacing around the big questions. "Um…Asuka," he began.<p>

"What?" Asuka asked, her face bearing a mix of tension and deep thought.

Taking a deep breath, Shinji prepared himself for whatever answers she could give. "What the hell is happening?" he asked quietly. "Why did Ayanami attack us? What's my father want me for? Why can I do these things I did back there?" he continued to ask, his voice raising in volume with every word.

"Quiet!" Asuka snapped at him. After a tense few seconds, she sighed and looked back at the road. "Look, I didn't mean to shout like that. But right now, I'm feeling very agitated." Taking a deep breath herself, she continued. "Those skills? That means you've been…activated."

"Activated?" Shinji asked. "What do you mean?"

"It's a long story…" Asuka replied.

"I think we've got the time," Shinji mused under his breath with a hint of sarcasm.

"Well," Asuka said, "you remember all those synch tests?" Looking over to see him nodding, she continued. "Turns out there was something else they did to us…subconsciously."

Shinji sat quietly, his eyes wide.

"They turned us into living weapons," Asuka said, her expression dropping slightly. "Very useful for taking care of problems quietly."

"What problems?" Shinji asked.

"People standing in the Committee's way," Asuka replied. "And the Commander's, too."

"Committee?" Shinji questioned.

"NERV's not quite on the top of the food chain," Asuka explained. "The Commander's been working with this twelve-member cabal called SEELE. They're the real force behind the EVAs."

Shinji took a moment to take in what he'd been told. "So that makes my father as much of a tool to them as us," he said.

"Heh, they wished he'd been that obedient," Asuka said.

"What do you mean?" Shinji asked.

Sighing again, Asuka continued. "You'll get the full story in a while. But for now, let's just say NERV and SEELE had a much darker purpose. And we were just pawns…" Shaking her head, she resumed speaking. "What they were planning was very different that what your father had in mind. And to that end…"

"…he used us," Shinji finished. "It's not just me, then. No one means anything to him."

"Not really," Asuka interjected. "It was the Committee that used us, the Commander has the First to do that for him."

"So that's why she attacked us?" Shinji asked.

"Yeah," Asuka answered. "And as for why the Commander's wanting you alive…Unit-01's needed for his plans, and ever since it ate the 14th Angel and absorbed you, it won't work except for you."

"Not even the Dummy Plug?" Shinji asked, remembering the infernal device.

"No one," Asuka said, her tone flat. "You were part of something so big it's frightening…and everyone but him and the SEELE had no clue."

Shinji pulled his legs up to his body and crossed his arms over his knees. "I never wanted any of it, you know?" he said. "All I wanted was for him to acknowledge me…"

"I know," Asuka said, her voice softening. "And after all that teasing about 'the invincible Shinji Ikari'…I never would have guessed. I was always just expendable…"

Noticing her change of expression, Shinji decided to tell her where he'd been. "I don't remember how I got there," he started, "but I was pulled out of the sea around Tokyo-2 just over six weeks ago. Woke up a week-and-a-half ago to find out I'd been found in an outfit like the one Rei was wearing, shot twice in the back, one of them hitting that 'chip', and unaware what had happened." He took in a deep breath and began again. "The crew let me off at Tokyo-2. I walked from there back to the apartment, all the while noticing these strange lines of thought I'd never had. And then…well, you know the rest."

Asuka sat in silence, listening to her roommate's story. When he finished, she spoke up. "Yeah…up until earlier, I thought you'd died," she said.

"What about you?" Shinji asked, concerned. "Last time I saw you…" he trailed off, remembering how she'd been after the 15th Angel's attack on her mind.

"I've been better, if that's any comfort," Asuka said, she trying to hold back the same memories. "They activated me a few days after you disappeared."

"You keep saying 'activated'," Shinji cut in. "What does that mean?"

"That chip that was in your back?" Asuka asked. She glanced over to see him nod. "That's what it's for. It triggers the implanted skills we've got. The Committee could even keep us on target with it."

"You mean they were…controlling us?" Shinji asked, the anger in his voice evident.

"Yes, to some degree," Asuka continued. "They almost made me do something unforgivable…" The redhead's eyes were threatening to tear up, no matter who was looking.

Shinji placed an unsure hand on her shoulder, trying to calm her. "Asuka…what happened?"

Asuka hit the brakes on the car hard, shaking and trying to hold back the emotions. "Misato…" she said, barely above a whisper. "They were going to have me kill her!" she finished with a shout of anger and sadness.

His eyes going wide, Shinji gave her shoulder a small squeeze. "Tell me everything…" he requested.

Asuka gathered her composure and began to speak, her voice just barely even. "Like I said," she started, "it was almost a week after you'd disappeared. All I remember was being in the locker room at NERV and then it all goes sideways. Next thing I know, I'm standing in front of Misato with a gun in her face! She never even looked scared, like she was expecting it…"

Shinji could only listen in silence at her story, a faint reminder of something tugging at his mind.

"And," Asuka continued, "I…I just couldn't do it. Misato was one of the few people who really cared about me. I couldn't do that to her…" Asuka sniffled back a few tears that had almost fallen. "I broke down there in front of her, one of the few times I cried. Then I guess she got it in her head to knock me out cold," she said with a hint of annoyance. "After that, I woke up to the sensation that part of my back was being cut open and something removed."

"She knew about it?" Shinji asked.

"Oh, she knows about a lot more than that," Asuka said, her tone evening out again. She then started the car up again and resumed their drive.

"You mean she's okay?" Shinji questioned, feeling some weight leave his person.

"Where do you think we're going? She's been hiding out with me since," Asuka replied. Noticing the wide smile he was wearing, she spoke up. "What's with that grin?"

"I'm just so glad to hear you're both alive," Shinji said, wiping some tears from his eyes. "It was one of my main worries since I came to. And then finding the apartment like it was…"

"Heh," Asuka said, feeling her usual mood return, "there's no need to worry about the great Asuka Langley So-"

"No," Shinji cut in. "I was deathly worried about both of you. I just didn't know if you were alive or not."

Asuka could only look at her roommate, his concern for them surprising her. 'Heaven forbid I'd ever tell him, though,' she thought. "That's really all I can tell you for now," she began again, "you'll get the full details when we get there."

"Get where?" Shinji asked.

"Where Misato and I have been hiding since…then," Asuka finished. The occupants of the car falling silent again, the redhead put her foot down on the gas, hoping to get there before night fell…

* * *

><p>A few hours of highway travel later, Asuka pulled the black car into an off-road path. A mile or two into the side road, they reached the side of a cliff. "Um…are we here?" Shinji asked, not seeing any way further.<p>

"Yeah," Asuka said, getting out of the car and walking up to the cliff. Removing a small card from her pocket, she swiped it through a small crack in the surface. Slowly, a fake section of the cliff moved to the left and provided barely enough room to move the car through. Getting back into the vehicle, the redhead noticed the boy's odd expression. "Neat trick, huh?" she asked, a smirk on her face.

Shinji could only nod dumbly for a few seconds. As she pulled the car into the opening, he turned to Asuka. "How in the world did you find this place?" he questioned.

"Let's just say an…old friend left it to Misato and I," Asuka said, a hint of sadness in her voice.

The two teens stepped out of the car once Asuka had parked it and closed the false wall. Shinji took in the new scenery. The place seemed to be quite old, probably pre-Second Impact. The walls were a dull grey, with florescent lights recessed into the ceiling. It smelled of old machines and even older paint. "What is this place?" he asked.

"We figure it's an old fallout shelter," Asuka explained, walking ahead of him down one of the halls. "Dunno how long it's been here, but it survived Second Impact…so I guess that's good enough." Finishing with a shrug, she led her fellow pilot into a small room.

As he looked about the room, Shinji noticed nothing strange about it. A neatly-made bed and a table were all it contained. One of the doors in the room led into a shower, something he didn't have in his old room. Looking into the small closet, he was met with the sight of what few possessions he owned. His clothes were hung up, his cello propped up neatly in a corner of the small space, and his S-DAT player was sitting on the single shelf inside. "So that's where it all went," he thought aloud.

"Yeah, Misato grabbed it all after…" Asuka trailed off, both remembering what she'd told him earlier. "Anyway, " she said with a shake of her head, "I think she'd like to know you're alright." Nodding, Shinji followed her down the hall they had been standing in and into a larger room. In the center was a large table, easily big enough to be used for a dinner party. On one side were a few things, like a refrigerator and other basic kitchen appliances. On the other side of the room, however, he saw a line of large computers, not unlike some of the rooms at NERV headquarters. Nearby were several consoles and projection screens. 'I guess this was the operations room,' he thought idly.

Asuka crossed the large room and knocked on a door. "Misato," she said quietly. "You awake yet?"

Opening the door slightly, the former major tried to put on her best I-didn't-just-roll-out-of-bed face. "Oh good, you're back," she said with a smile and giving a heavy sigh. Looking behind the redhead, the older woman's heart caught in her throat as her eyes locked at the room's other occupant. Instantly snapping into the waking world, she walked past the girl and towards the boy. "Oh my God," she managed, staring with wet eyes at her other charge. Tackling him with a tight hug, she could only sob a word here and there.

Shinji, meanwhile, was a bit uncomfortable with the sudden attention. Misato had hugged him before, but never quite with this much force. The knot in his stomach, though, had since loosened at seeing her again. Getting one of his arms free, he returned the hug as best as he could. "I'm glad to see you too, Misato," he finally spoke, small tears forming at the corners of his vision.

From across the room, Asuka looked at the scene with a mixture of annoyance and relief. Annoyance at Misato's display, relief that her guardian was finally smiling again. The redhead was also relieved that Shinji was alright…but she squelched that thought down just as soon as it had come up.

Wiping her eyes and sniffling, Misato released him from the hug. "Sorry," she weakly said, "I'm just so glad you're alive…" Running a hand down his back, she felt the stitches of where his chip would be. "You removed it already?" she asked, turning in Asuka's direction.

"No," Asuka answered, shaking her head. "One of the shots hit him in it."

Nodding, Misato stepped back from the boy and gave him her brightest smile. "Just good to know they don't have you," she said, trying to regain her composure. "You told him?" she asked the redhead.

"Not all of it," Asuka said, taking a seat at the large table in the center of the room. "I left the biggest part for you."

"Of course you did," Misato said under her breath. Taking a seat herself, she motioned for the boy to sit as well. "I'd recommend it, this'll take a while," she told him. After Shinji seated himself across the table, she spoke up. "Okay, tell me everything that's happened."

Shinji took a deep breath and went back over the same story he'd told Asuka earlier, including the events in Tokyo-3. After he finished, the three sat in silence for a long while. "Now tell me what was left out," he finally asked after some time.

Misato sighed. "First, let's start at the beginning," she began. "You remember the 'truth' about Second Impact that NERV told you?" Shinji nodded. "Well," she continued, "that was just another lie. Truth is…the Committee discovered Adam and experimented with its form. That experiment failed…horribly. That's what caused it."

Shinji felt his hand begin its usual ritual of opening and closing. "So all this was SEELE's fault…"

Nodding, Misato resumed her explanation. "Long story short, they established Project E and what was to become NERV to further the Human Instrumentality Project…"

"The what?" Shinji asked.

"Essentially," Misato answered, "the main goal of SEELE and Commander Ikari. The process of all souls becoming one." She leaned the chair back slightly, her face a mix of anger and fear. "Third Impact…"

Shinji's eyes widened as much as they could. "Th-that's insane," he said, feeling his anger build. "Why would they do that?"

"To them, this world is stained with too much sin to continue," Misato said. "Being one with God and all life seemed a better plan than living to them."

The room fell silent again as Shinji took in what he had been told. "So…this is why I'm needed?"

Misato shook her head. "No…the Commander has something different in mind." Seeing his curious look, she continued. "Something was taken from him a long time ago. And he'd reduce everything to nothing just to see her again." She looked up at Shinji. "You know who I'm talking about, right?"

Shinji's expression fell as he realized who. "Mother," he whispered, barely audible. "So she was there all along…"

Misato blinked a few times, her surprise obvious. "Wait…you knew?"

Shinji shook his head slowly. "Not until I was absorbed into Unit-01. I saw her there," he said, his head descending to rest on the table's surface. "Goddamn you, father…you never told me."

Misato placed a reassuring hand on his back. "I'm so sorry…" she said softly.

Asuka watched with a clear look of sadness on her face, the scene before her a mirror-image of when Misato had told her of Unit-02's secret a couple of weeks before. 'Mama…' she thought, a small tear escaping her eye unnoticed.

Holding in his tears as best as he could, Shinji looked back up at Misato. "How did you learn all this?"

Misato's expression hardened, a look of concentration on her face. "Some of it I found on my own," she said, her gaze looking not at Shinji, but something past him.

"And some of it she had help with," a man's voice came from behind the Third Child. Shinji's expression went from sadness to shock, recognizing the voice instantly. He turned around quickly to catch sight of the familiar grin of Kaji Ryoji. "Long time no see, mister Ikari," he told the boy, bowing slightly.

"Ah good, you're up," Asuka said with a smirk, not quite in her usual tone when seeing the man.

Misato said nothing, only giving her one-time lover a wide smile.

Shinji, on the other hand, was suddenly caught by a flood of images. A gun in his own hand…a fan…that grin on Kaji's face…and the same pain he'd woken up to. Clutching at the sides of his head, the boy slumped out of the chair and onto the floor. Landing on his knees, he was unable to hold in tears of pain and sadness. "Oh God…" he spoke softly, "I remember…"

"Sorry, Shinji," Misato said, crouching down and placing her arms around him. "It was the only way to jog your memory."

Asuka sat quietly, watching the scene unfolding with an evident look of sadness on her features. She had agreed with them that this was the only way…but the look on his face still hurt her. She had gone thought that herself not too long ago.

Picking himself up from the floor, Shinji sat back in the chair he'd occupied just a few minutes ago. Wiping his eyes with the back of his hand, he looked back to Kaji, who was now seated at the table. "Then that means…"

"Yeah," Kaji said sadly, "SEELE sent you to eliminate me." Taking a pack of cigarettes from his shirt pocket, he lit one of them and took a long drag before continuing. "What happened wasn't too far from what happened when they sent Asuka after Katsuragi," he explained, exhaling a cloud of smoke.

"I couldn't do it. You were the closest I'd had to a father figure," Shinji admitted.

"Heh, I'll take that as a compliment," Kaji said. "Sorry for shooting you, by the way. And with your own gun."

"No real harm done," Shinji replied. "One of them hit my chip, actually."

"No shit?" Kaji asked. "Well, that's something…" His expression returned to serious. "No really, I'm very sorry. I was hoping you were alright, but at the same time I thought…if you were gone, both the Committee and the Commander's plans would be undone." Looking at the boy, he continued. "Just made a snap decision. Never been this glad to be wrong."

Shinji felt no anger at the thought that Kaji had tried to kill him. It made sense, after all. Without him, Unit-01 couldn't work for anyone. "How did I end up at sea, then?" he asked the older man.

"Simple enough," Kaji answered. "The docks were near where you found me. I just dumped you there. Like I said, I hoped someone would find you soon…"

As the room fell silent again, a beeping from one of the consoles caught Shinji's attention. "What is that?" he asked, walking over to it.

"Perimeter alert," Asuka replied. "Someone's outside."

Looking at the screen, Shinji caught a glimpse of a familiar school uniform and distinct hair color. "Ayanami…" he said, his voice barely above a whisper. He then looked to Kaji. "Got a gun I could borrow?" he asked in a cold tone.

"Uh…sure," Kaji replied with a look of confusion. "But why?" he questioned, handing the boy his handgun.

"Got something to take care of," Shinji said in the same icy voice.

As he walked towards the exit, Misato called out to him. "Where the hell are you going?" He ignored her, his pace quickening. The older woman looked puzzled for a moment before she put the pieces together. "Asuka, you didn't tell him yet?" she asked in a panic.

Asuka considered her question for a second before her eyes went wide. "Shit!" she yelled, running after the Third Child, hoping she could avert what might happen.

* * *

><p>Shinji opened the false wall to come face-to-face with the First Child. Who, not twelve hours before, had tried her damnedest to bring him back to NERV. "Ayanami…" he said, his voice an odd reflection of his father's.<p>

"Ikari," Rei said, her familiar calm expression in place.

His hand shaking slightly, Shinji raised the gun at her. "Just turn around now and you'll live."

"I do not understand," Rei stated.

Grabbing the First Child around the collar and pinning her against the wall, Shinji put the barrel of the gun under her chin. "I will not go back there," he said, the calmness in his voice disturbing him. "You will leave now and tell the Commander you found nothing."

Rei's impassive face remained. "I do not think that is-"

"Shut up!" Shinji shouted. "You tried to kill Asuka and nearly killed me. I've turned my back on that machine," he said, referring to Unit-01. He took the safety off the weapon. "Now go. Or I will kill you."

A hint of fear flashed in Rei's eyes. "I would not do that," she said, no waver in her tone.

"And why the hell not?" Shinji asked loudly.

"Because she's not the enemy…" Asuka's voice came from his side. Misato and Kaji were right behind her, a long look on both of their faces.

"Wh…what are you talking about?" Shinji yelled. "Back in Misato's apartment…"

"…was a ruse," Asuka said in a small voice. "Meet our inside source."

Shinji suddenly felt sick to his stomach. He took the gun down from the pale girl's head and put the safety back on. Dropping the weapon with a loud clatter, he dropped to his knees. "Oh God…Rei, I almost…" he said, crying again. "I'm…s-sorry…" he got out between sobs.

Rei was unsure of how to react to this, only holding out a hand to help him up. "No. I am sorry for any misunderstanding," she told Shinji.

Wiping his eyes with one hand, Shinji took the girl's hand and stood again. "It's…alright," he said, the tight knot in his gut slowly easing. "That still hurt earlier, though."

"Hey, had to make it look good to anybody who'd have seen," Asuka said in a calm voice. Walking over to the First Child, she readied her words carefully. "First," she started. "Good to know you haven't gotten yourself killed."

Rei nodded. "And to you as well, Sohryu." Walking past the others, she entered the bunker with the other women following after a moment.

Shinji could only stare at what had just happened. 'Did…did they just have a non-hostile talk?' he asked in his mind, the very idea surreal after having watched what few times they had talked before.

Kaji picked up the gun he'd handed to Shinji. Noticing the boy's strange look, he spoke up. "Hmm? Something bothering you?"

Shaking his head, Shinji could only give out a weak laugh. "I swear, I could live to be a hundred," he started, walking back towards the hall, "and I'll never understand women."

As the boy vanished from sight, Kaji smiled at his words. "Yeah…you and me both," he said to himself, closing the false wall.

* * *

><p>The five of them having taken seats around the table, the conversation resumed. "Well then," Misato said, "where to start…"<p>

"I've got a question first," Shinji spoke up, turning towards Rei. "Why'd you go against the Commander?"

A silence hung around the room before Rei began. "I was created for a purpose," she explained. "I am just as important to his scenario as you and Unit-01 are. But…I have been given a different purpose as of late. And I do not wish to follow along with it anymore"

"And what's that?" Shinji asked.

Rei averted her gaze. "I…helped him eliminate SEELE."

Shinji's eyes went wide. "W…what?"

Taking a deep breath, Rei explained. "With your absence, the Commander was forced to accelerate his timetable. You see, the Committee had no need of you. Only Unit-01. To that end, he sent me to eliminate three of their members."

Shinji sat quietly, hanging on every word.

"My mission each time was simple," Rei continued. "Locate the target, learn his patterns, and dispatch them in a way that could not be traced back easily. I followed those orders to the letter."

"And like all men in power," Kaji cut in, "they began eyeing each other suspiciously. Even with their higher purpose, they still behaved like all politicians and dictators do."

"Indeed," Rei said. "The remaining members began to secretly send their own agent against others within. It took less than four weeks for twelve to become one. The last one left was Chairman Kiel, head of SEELE. Commander Ikari sent me after him last, telling me to make certain he knew it was me before finishing it." She fell silent after that, letting it hang for a few minutes.

"You mentioned an agent of theirs," Shinji interjected.

Rei nodded. "Yes. The Fifth Child, Kaworu Nagisa."

Standing and walking over to one of the consoles, Rei picked up a folder and placed it in front of Shinji. Opening it, he found several grainy pictures showing a grey-haired young man with ruby eyes. "He…he looks like you," he said to the First Child.

"We're still not sure about that," Misato spoke up. "Not even the computers at NERV have anything on him. And I mean nothing. So it's a possibility he's their version of Rei."

Rei walked back over to the console and gathered a couple of folders before sitting back down. "And with the Committee gone, the Fifth became the Commander's personal protection. I believe it is because he still does not fully trust Nagisa, and intends to watch his actions." Opening one of the folders, she slid it in front of Shinji. "And this also placed construction of the Mass Production EVAs in permanent stasis."

Shinji looked at the contents of the folder, mostly technical specs and pictures of assembly plants. "Mass Production?" he asked.

"EVA Units-05 though 13," Rei said. "The Committee intended to finish them and send them to retrieve Unit-01 to begin Instrumentality. The Commander has no need of them, so he simply halted their progress."

"And just what would he need?" Shinji questioned, his expression stone-like.

"Myself," Rei explained, "Unit-01, you, Lilith, and Adam."

The last name made Shinji feel like he'd been slugged. "Adam? The same that caused Second Impact?" Nodding, Rei moved the last folder in front of him. Opening it, he saw a picture of a giant white shape affixed to a cross and another showing an embryonic creature. "What…are these?"

"This," Rei said, pointing to the white shape, "is Lilith, the 2nd Angel. The Committee has kept it beneath headquarters long since before NERV existed. And the other is Adam in its post-Second Impact state."

"Why would they keep them there?" Shinji asked.

"I am unsure of why the location," Rei answered. "But Lilith was kept to be used in their ceremony after the Angels were finished. But that is not the case without the Lance of Longinus…"

"So that's why they needed Unit-01?" Shinji asked, remembering the weapon used against the 15th Angel.

"Yes," Rei said, gathering the folders. "But the Commander's plans do not require it. His was the only one that required Adam, though."

"And where is it?" Shinji questioned.

"Commander Ikari implanted it into his right palm as a means of controlling his version of Instrumentality," Rei explained. "I have heard the Commander say that there is still one Angel left, but I do not know its whereabouts."

"So I'll still have to use Unit-01 even if Father's stopped…" Shinji said under his breath. The room fell silent again, this time for quite a while.

"That is everything important," Rei said, "but there is one last thing you should know."

"What is it?" Shinji asked, his head already spinning with the information he'd been given.

"You are aware of why he is doing this?" Rei asked.

Shinji nodded. "He…wants to be with mother."

"Yes," Rei said. "To that end, he kept a reminder of his purpose." Turning to look at Shinji, she continued. "When I was created, I was given Yui Ikari's features…"

Shinji's eyes went wide and he began to tear up. "I knew there was this…familiar feeling around you," he said, the shock on his face becoming a small smile, "but I had no idea…"

Rei stood from her seat, walking to the door. "I am afraid I must return. I have been here longer than necessary."

"Rei, wait a minute," Shinji said, wiping his eyes. Standing and walking towards her, he put his arms around the girl. "Thank you," he said, "I needed to hear that. All of it."

"You are welcome," Rei said with the faintest hint of a smile. "I will keep in contact," she said to Misato as the boy released her. The older woman nodded back, her expression business-like.

As Rei resumed her trip out, Shinji called to her. "Hey." As she turned around, he gave her a serious look. "Take care of yourself…and watch your back."

Nodding, Rei made her way back to the false wall and out of the bunker. The trip back into the city would take a while.

Back inside, Shinji sat down at the table once again and hung his head. "That about answer everything?" Kaji asked him.

"Yeah…" Shinji said, a look of relief on his face.

Asuka had watched the scene unfold before her with some unease. None of the information had been new to her, save the fact that the First had been modeled after Shinji's mother. But it was just something about it all that made her feel…empty. And it wasn't the first time lately she's felt it…

* * *

><p>A few hours later, Shinji had managed to eat and get a shower, a couple of things he hadn't had the luxury of in nearly two days. Feeling the water run over him, he went over the explanations he'd been handed again and again in his mind. He knew what he had to do, the only real question being was he ready or not. Sighing heavily, he turned the water off and grabbed a towel.<p>

After drying and dressing in a pair of dark-blue short and a medium-blue shirt, he exited the shower to find Misato in the room he was using. "Hi Misato," he said.

Misato was seated at the foot of his bed, her face carrying a worried smile. "Hey," she said. "How're you feeling?"

"Better now," Shinji answered, laying out on the bed. "A meal and a shower helped. Cleanses the soul as well as the body, remember?"

Misato continued to smile at her own words coming from him. "Sorry to just lay it all on you like that," she said.

Shaking his head, Shinji sat up. "No, it's okay," he told her. "I did need to know. I just wish I knew what to do now…"

"For now," Misato said, standing from his bed, "we continue to hide here and listen out for anything. We've got a lot of bugs planted around headquarters. We'll know what they know." Opening the door, she turned back to him. "Just try to relax for now. You've earned some rest, after all." And with that, she walked out of the room.

Shinji smiled to himself, despite his internal confusion. Just being around them again made the last several days worth the trouble. But the bigger things at hand still persisted in his mind. Trying to shake the thoughts loose, he walked over to the wall and turned the lights off, picking up his S-DAT player on the way back. Putting the earbuds in, he hoped the device would help to ease his mind for a while.

Lying back on the bed, Shinji pressed play and waited for sleep to come…

* * *

><p>In the room she'd chosen, Asuka sat on her bed. Unable to sleep, she had paced about the area for a while before looking for something to take her mind off the last two days. Shinji's reemergence into her life had brought back the confusing mix of emotions concerning the Third Child. After all she'd learned about NERV and SEELE, she felt some regret at her treatment of the boy. Not that she would be telling anyone that, not even out loud to herself.<p>

Looking about the room, the Second Child took in the amount of workout equipment it contained. The room must've been the gym at one point, she figured. Asuka had taken it because it was the largest, so of course she wanted it. And working out here had kept her mind off the many things that should've been occupying her thoughts. But with him there…

Shaking her head, Asuka began punching the large bag hanging in the center of the room. And while doing so, her thoughts wandered to her fellow NERV deserters. She'd made a small measure of peace with the First, and seeing Kaji again had made her feel somewhat better…especially considering what she'd almost done to Misato.

Giving the bag a hard kick, Asuka was beginning to become frustrated. This usually worked well enough to get the thoughts out-of-mind…so why not tonight? "Of course, it's obvious why. He's here," the redhead said in the dim light of the room.

Then Asuka began to feel some of her old self come back. A smirk crossed her face as she figured out a new 'test' for the Third Child. Most definitely not like the last one she'd tried, anyway…

* * *

><p>Shinji had put away his S-DAT player and was just about to doze off when a small knock came from the door to the hall. Standing from the bed, he walked over and opened it. As he did, his vision was filled with a redheaded form. "Oh, hi Asuka," he said with a smile. "Did you want something?"<p>

Asuka stood at his door, dressed in a black workout top and red sweatpants. "Yeah, come with me for a bit," she said, motioning for him to follow.

Shinji stood in place for a few seconds, his eyes blinking repeatedly. 'Now what in the world would she want?' he thought. "Uh…sure," he said, following her down the hall and into another room. This one contained several pieces of workout equipment and a bed. "This is your room?" he asked.

"Yeah," Asuka said in a haughty tone, "I figured it would keep me busy. And a girl like me needs the most room…"

"Uh-huh," Shinji said, tuning her out.

"Hey! Listen when someone's talking to you!" Asuka said with a hint of annoyance. "There's something I'd like your help with."

Shinji blinked a few times. He had rarely ever known Asuka to need help with anything. "Sure, whatever you want."

"Alright then," Asuka said, placing her hands on her hips and spreading her feet. "I'd like you to fight me."

Shinji's expression dropped sharply at the words. "W-what?"

"I didn't stutter, dammit!" Asuka shouted. "Come on, I'd like to see how good you are with those…skills."

"Y…you're serious?" Shinji asked, almost wanting to pinch himself to see if he was dreaming.

"You're goddamn right I am!" Asuka said proudly. "Besides, I've got some anger to work off…"

Regaining his composure, Shinji shook his head. "That's just crazy. I don't want either of us to get hurt."

"Oh, you don't get to back out of this," Asuka said, putting her left foot down hard. "It's just a sparring match. No need to take any of it seriously."

"What about Misato or Kaji?" Shinji asked. "Won't they hear?"

"Not a chance," Asuka said, knocking on one of the walls. "This room is soundproof when closed up."

Shinji didn't really want any part of this, but he couldn't find a way out of it. And he did have to admit, he needed to get in some practice with his new hand-to-hand skills. "Okay, fine," he said with a sigh. "Just this once."

Asuka's expression hardened at those words. Getting into a stance, she motioned to Shinji. "Alright, stand a little closer," she said.

Shinji walked over until he was only a couple of feet from her. Readying himself into a similar stance, he spoke up. "Ready when you are."

Asuka smiled internally to herself. 'Good to see him get into this,' she thought. Stepping forward, her first move was a straight left punch…which Shinji easily sidestepped. But he was caught by the same hand being swung backwards after. The redhead then went to work with her feet, trying to land a kick on the Third Child.

Shinji backpedaled quickly, blocking her lithe legs and looking for an opening. Seeing an opportunity, he quickly dropped and grabbed the leg she was balancing with. The Second Child landed with a thud, but quickly sprang to her feet from her palms.

"Good move," Asuka complimented. "But I'm not even warmed up." Rushing at him, she gave a sharp blow to his chest and grabbed his left arm. Using her momentum, she almost threw him across the room.

Shinji grunted in pain, but rose to his feet again. Unfortunately, just in time to see Asuka jump at him and wrap her legs around his neck. Landing with her hands on the floor, the redhead pulled him back to the ground. Getting herself upright again, she looked down at the boy, a feeling of superiority nearly giving her a high. "Get up," she spoke in a ragged voice. "Not even at half-way yet."

Shinji took his time rising, his neck sore and ribs aching. 'She's really serious…' he told himself. Deciding to go on the offensive, he closed the distance and grappled with her for a few seconds before getting a grip on her arm. Using his leg, he swept the girl's legs out from under her and pinned her to the floor. "Ha…" he said, trying to catch his breath. "I win."

Asuka said nothing, only smiling a dark grin at Shinji. Her arms quickly wrapped around his neck and she hefted his weight over her, the boy landing on his back with a hard smack. Before he could get up, the redhead grabbed him by the collar and dragged him to his feet. Once there, she gave him several hard blows to the sides, finishing with a straight-up kick to the jaw.

Shinji landed on his butt again, now in serious pain. At first, this had seemed like training. Now she seemed to be out for blood, his this time. "Okay…that's…enough," he said between breaths.

"No! Get on your feet and back into the fight, you pussy!" Asuka roared. To make her point, she put a hard foot into his left knee. "Don't make me kill you…" she threatened in a low growl.

Shinji pulled his leg out from under her foot and stood up. As Asuka came at him again, he decided this had gone far enough. Blocking her next punch, he took the girl's slender wrists into his grip and pinned her to a wall. Placing a foot over both of hers, he spoke again. "Asuka!" he yelled. "Enough!"

Try as she might, Asuka was held fast by his hands and foot. "Get off me now!" she spat, wriggling to free herself.

"No," Shinji said, his voice calm now.

The look on his face stopped any more of Asuka's attempts to free herself. Here was that hidden strength she'd seen before, all because of her this time. Relaxing in his grip, she panted heavily and felt the sweat almost pour off her skin.

Shinji wasn't much better, nearly everywhere on his body in pain, his breathing ragged and drenched in sweat. But he still kept his eyes on her, watching to see if she would resume her attack. When it was clear she was done, he released her wrists and feet. But he didn't step back.

Right then, both teens looked each other in the face, the same mixture of emotions in one evident to the other.

Pain. Hate. Fear. Loss. Sadness. Determination. Confusion.

Hurt…seeking comfort.

Slowly, both the Second and Third Children inched themselves closer to the other.

Heaven help them for whatever was to happen.

*******To be continued…*******

**A/N:** Well, that's roughly sixty to sixty-five percent down, only another large chapter and a medium epilogue to go. A lot happened in this part, yes indeed. And, of course, my other main theme just came up. Like I could write something without it…

Oh, and that ending? I know…I'm terrible and a cheap tease.

And it's not the first time, you'll recall.

You're welcome. ^_^

*******Omake time!*******

The camera pans into the author's room. At the computer isn't him, but Mitsumi. Wearing a tiny pair of headphones and looking over the first two chapters of this work-in-progress.

Mitsumi: Hey, this ain't half bad. Different from the rest, too…

As she read down to the end of this part, a slight blush came to her as she realized where it was headed.

Mitsumi: (shouting and removing her headphones) BAKA! I THOUGHT I MADE IT CLEAR!

Bard: (poking his head into the room) Ah…get to that point, did you?

Mitsumi said nothing, only fuming and staring daggers in his direction.

Bard: (sweating) Oh come on…trust me on this. (holding up a piece of paper) Here's the overview for the next part, you can take a look yourself.

Grabbing the paper from him, Mitsumi looks it over carefully.

Mitsumi: (sighing) Okay…fine. As long as it's for the story…

Bard: It's ALWAYS about the story, you know that. You know I don't write smut…

Mitsumi: (blushing at that last word) And you'd best not… (opens her tiny purse and pulls out a VERY large warhammer) …or else you'll get the business end of this. Are we clear?

Bard: (nervous) Crystal.

Mitsumi: (smirking) Good. Now I think I'll go practice a little.

Placing the hammer back into its compartment, Mitsumi floats out of the room and into hers.

Sighing, the author plops down in his computer chair.

Bard: (whispering to the camera) Now if any of YOU would like to fill in the above or that "missing piece" of TLaWR, I won't stop you. But let's just keep it quiet, okay?

As the camera pans away, we hear the chords to "Vision Thing" start up.

*******End Omake*******

Pre-read for this chapter was again done by the team of Dark Machine, Eric Blair, gesser87, and JimmyWolk. Good work as always, gentlemen.

Small note: this chapter and all previous/following it were written around late June/early July last year. So a quick "sorry" to everyone who may have been waiting for something after TLaWR. Revisions and pre-reading can take quite a bit of time, it would seem…

For any of you who are new to the community, all of my older (2004-2006) works have undergone a small bit of tweaking (as of the 14th of June 2010). So go take a look, tell me what you think. And review! Even if it's not positive, review!

As usual: good comments will be appreciated, bad ones will be ignored (or kept for firewood). But I do favor good/helpful criticism, so send it my way!

**-AngelNo13Bardiel-**


	3. Uprising

See Chapter 1 for disclaimer.

**THE IKARI IDENTITY**

Chapter 3: Uprising

* * *

><p>Asuka slowly awoke into the darkness of her temporary room. As the grogginess left her, she noticed a couple of odd things. One, she was head-to-toe sore. The other was that she was lying on something warm. Running a hand over the surface, she could swear it felt like…skin.<p>

A groan nearby caused her eyes to snap open. Asuka suddenly realized the object had been someone else. Then she remembered the night before. 'Oh no,' she thought.

Fumbling for the light switch on the wall near the bed, Asuka flipped it. As the florescent lights flickered, she was met by the sight of Shinji, lying in her bed and rubbing his eyes. He had several bruises she could see on his shirtless torso, evidence of the training last night that had become a real fight. Both looked at each other, their expressions ones of slight shock. "Uh…Asuka…" he started, his face as red as her hair.

Asuka slowly rose from the bed and sat up, hanging her legs over the side. Her heart pounding, she spoke up. "D-did we…" she tried to ask, unable to free the words.

"Y-yeah," Shinji managed to answer, his throat tight.

"Oh God," Asuka repeated several times, her head in her hands.

Shinji sat up, his shock becoming sadness. "I'm sorry…" he said, curling himself up and holding his arms around his legs. "I'll go."

Asuka looked back at him, trying to hold in a few tears. "No," she said, "you aren't the only one to blame for…this."

"What?" Shinji asked, turning his head towards her.

"I mean…" Asuka looked for the right words, shaking her head. "It wasn't like you took advantage of me, we were both willing." She dropped her gaze, staring at the floor. "I shouldn't have even gone to your roo-"

She was cut off as Shinji placed a hand on her shoulder and gave it a squeeze. "Asuka…" he started, "I want you to know something." As she looked up at him, he continued. "I don't regret it at all."

Asuka cast her sight downward again. "Of course you don't," she said in a quiet voice. "You're male, you got laid-"

"No, that's not it at all," Shinji interrupted, his tone serious. "I don't regret it because…it was you."

Asuka felt a knot in her stomach form, but she stayed quiet and turned away from him.

"I was always interested in you…I just never found the words," Shinji said, edging over to her and placing his arms around her neck, leaning against her. "But last night was something special. Something I'll never forget. But the main reason I couldn't possibly regret this is because…" He leaned in and whispered the rest in her ear, just barely audible to her.

Asuka felt tears run down her cheek, but she made no effort to stop them. "Idiot…" she said, "you can't take back saying things like that."

"I don't want to," Shinji replied, leaning his head against the side of her neck. "But…we were kinda reckless. I don't think either of us could help it, though."

"I know," Asuka said. "With all that's happened lately, and the both of us high on adrenaline and looking for an outlet…"

A long silence settled in the room. "So…what now?" Shinji asked.

"I…I don't know yet," Asuka answered. "It's just all so…sideways. I mean, it's not like I hate you or anything…ah damn it to hell, I'm confused!" she said, sighing heavily.

As Shinji was about to open his mouth, the sound of the door opening brought their attention to it. "Come on Asuka," Misato's voice came, "you can't just sleep all da-" Her words left her as she saw the two of them. Blinking a few times, she slowly exited the room, closing the door.

Asuka and Shinji sat in the awkward silence for a moment. "You…think she knew?" the redhead asked.

"I don't see how she couldn't," Shinji answered while moving back to the spot he'd been in, his face beet-red, "you're…um, still naked."

Asuka suddenly realized this fact, yelping and wrapping the sheet around her body. "And why the hell didn't you tell me earlier?" she asked, annoyance and anger in her tone.

Shinji didn't reply, looking away from her. "I should go now," he said after a minute of silence. Pulling his shorts and shirt back on, he rose from the bed.

As he was about to step towards the door, Shinji felt Asuka grab his wrist. "Hey, wait a sec," she said, making him turn back to look at her. "I…don't regret it either," she said with a small smile. She seemed like she wanted to add something else, but the words seemed to not be able to flow, before she turned away and added, blushing, "I..."

Shinji returned the smile as best as he could. "It's alright, you don't have to say anything," he said, face flushed again.

"I think I just need some time to figure this out, okay?" Asuka asked, shaking her head. "It's just…confusing."

Shinji continued to smile at her, taking his hand from her wrist and giving her own hand a small squeeze. "Take as long as you need," he said, releasing her hand.

As he stepped out of the room, Asuka felt the tears resume again. 'All I wanted,' she thought, 'was for him to hold me and not leave me alone. And then he goes and says something like that…' Shaking her head, the Second Child stood from the bed and headed for her shower…

* * *

><p>Out in the hallway, Shinji was returning to his room when he caught sight of Misato waiting near his door. "Um…hi," he managed weakly.<p>

Misato turned her head towards him, her face serious. "Okay, I don't think I have to," she began, "but I'm going to ask anyway: was that what it looked like?"

Swallowing hard, Shinji prepared himself. "Yes," he answered.

Misato looked at the floor. "What the hell were you two thinking?" she asked.

Shinji shifted his weight between feet, feeling very nervous. "I know, but I never intended for any of it," he started, "it just started as a practice fight, and then…I don't know. That's just what happened."

"You're both going to make me old before my time," Misato said, trying to smile a little.

"I know, I'm really sorry…" Shinji said. "I'm willing to take responsibility, if that's what you want me to say."

"I know you are," Misato said, leaning against the wall. "Just as long as you're willing to admit it."

As Shinji walked into the room, Misato spoke up. "And I can't really judge you fairly as children. You've both been through more than almost anyone, let alone any adult. I'm sorry I couldn't stop them from taking that away…" Standing from the wall, she walked towards her own room. The Third Child stripped and stepped into the shower, turning the water on and feeling it run over him. The previous night had opened his eyes to a lot…and not just about Asuka. He had laid in the dark after she fell asleep, thinking about his father's plans and his place in them. He knew what he had to do now…he just needed the right approach.

* * *

><p>Having dried and dressed himself, Shinji left the room and walked into the large center room to see the other three sitting about the large table. "Morning," he offered. Asuka gave him a weak smile, which he returned. Turning to Kaji, he continued. "Hey Kaji?" he asked with a serious face.<p>

"Hmm?" Kaji said. "Something you need?"

Sitting down to the table, Shinji took a long breath before answering. "I think…I'm ready to finish this. It's time."

Kaji's smile gave way to his own serious look. "You sure about that?" he asked. "This is going to get pretty hairy from here on out…"

Shinji nodded, his own expression unwavering. "I understand. But…the Commander needs to be stopped. No matter what."

Misato gave the boy her best smile. "I'm proud of you, Shinji," she said. "But this is some deep water we're treading."

"I know," Shinji told her, "But I meant that…no matter what."

"I'm glad to hear that," Kaji said. "We've had the beginnings of an operation for a week now. But then we heard from Rei that you'd been spotted, so…"

"…so you've been waiting for me, then," Shinji finished.

"Yes," Kaji replied. Standing and walking over to one of the consoles, he inputted several sets of keystrokes. As he punched in the last few, the large table lit up with a diagram of NERV headquarters. "Okay, this is what we've got so far," he began. "We'll have to get back into the city, for one. Then the best way down into the Geofront would be this one," he said, punching in a few keys to pull up the elevator that was nearest to headquarters. "After that, it'll have to be kept as quiet as possible. Or we'll be swarmed by whatever security is left…"

"What do you mean?" Shinji asked.

"NERV's mostly down to a skeleton crew now," Misato explained. "With the Committee gone, the Commander doesn't need more than what's needed to protect the main areas of headquarters and run maintenance. Security's only about twenty or thirty, and only the main bridge crew and what's needed to maintain Unit-01 remain. Section Two would be a worry, but they're currently stretched thin throughout Tokyo-2 and Tokyo-3 looking for you."

"That's one small mercy for us," Kaji mused. "But, of course, there's still the Fifth…"

"Yeah, him," Shinji said. "He'll be protecting father."

"And as far as we know," Kaji said, pointing to Shinji and Asuka, "he's trained the same as either of you."

"He'll be a hell of a challenge," Asuka spoke up.

"Well, there's always Rei, in case things go south," Misato said.

"What about surveillance?" Shinji asked. "I mean…they'll have to see us coming."

"That's actually the easy part," Misato replied. "Ritsuko's taking care of that. She's got a little something in the MAGI's programming that'll knock out any bit of video around Tokyo-3."

"Doctor Akagi is in on this?" Shinji questioned.

"Of course," Kaji said, "she'd like to see him burn just the same as us. She did destroy the Dummy Cores, right?"

"I guess," Shinji said, "I just don't understand why the Commander's still keeping her there after that…"

"You know why," Misato said. "The Commander still needs her to finish his plan."

"And as long as she's willing to go along, he won't dispose of her," Kaji said. "And we'll still need to get her out of there, too."

"Huh? I don't understand," Shinji said.

"Regardless of whatever secrets between us," Misato began, leaning back in her seat and looking sad, "she's still an old friend to me and Kaji. We can't leave her to that fate."

Shinji remembered when he'd nearly said those same words to Asuka in the apartment days ago. "I see," he replied. "But what about the last Angel?"

The table fell silent at that. No one really had a clue when it would show. "I guess…the only thing we can do is stop the Commander's plan and then take back control of NERV," Misato finally said. "Then after it shows up, we can take care of it and then we'll just wash our hands of it all."

Shinji nodded. "I only have one thing to ask of you all, though…"

"What's that?" Kaji asked.

"When we get back inside headquarters," Shinji began in a cold tone, "I'll be the one to take care of the Commander. I want none of you involved."

"You need revenge that badly?" Asuka questioned.

"Not revenge," Shinji replied, shaking his head, "closure. It has to be done." He had already made peace with that fact since the other night. But it still had not settled in his mind well. 'I can't stop hating him for any of it,' he mentally noted.

"I understand, Shinji," Kaji said, walking over and placing a hand on the boy's shoulder. "I just hope you do." Turning towards Misato, he spoke again. "Gather what we need, it's going to be a long night."

Nodding, Misato unseated herself and headed for the hall near her room. Asuka followed her after a second, stopping to give Shinji a ready-but-weary look. He smiled to her as best as he could given the room's atmosphere. Turning towards Kaji, he nodded. "What do you need?"

"Follow me for a minute," Kaji said, "gotta gather some gear for one last mission…"

* * *

><p>Several hours later, the four of them were piled into Misato's car and heading back towards Tokyo-3. Kaji, Misato and Asuka had opted to wear black fatigues, while Shinji remained in his old school uniform.<p>

"Why wear it?" Asuka had asked him.

"So I'll stand out," Shinji had answered. "That way, there'll be no doubt it's me."

Now the two sat quietly in the back seat of the car, mentally preparing themselves for what was to happen. There would have to be blood and death. How could they avoid it this time? It was kill-or-be-killed. No mercy would be shown, so no quarter would be given.

Asuka was snapped out of her reverie by a warmth on her hand. Looking over, she saw Shinji's hand on hers and a smile on his face. "We'll be just fine, right?" he asked quietly.

"Yeah…" Asuka replied with a whisper, squeezing his hand a little. She wasn't really convinced, but his faith in them did help her a bit.

After making it to the edge of town, Misato pulled the car into the forest to hide it. From here, they were going on foot. "Everybody put these in," she said, giving the others earpieces. "Two-way mic, just press the button on it to talk."

Placing the item in his ear, Shinji opened up the trunk to find what they'd gathered at the bunker's armory. Taking a submachine gun and a handgun, he slung the larger weapon around his shoulder and put a couple of clips for the smaller one in his pockets. Handing out the same to the others, he walked over to where Kaji was standing. "Okay, now what?" he asked quietly.

Nodding, Kaji pressed the button on the earpiece. "You there, Rits?"

* * *

><p>Deep inside of NERV headquarters, Ritsuko Akagi sat in her office. She heard the voice coming from her own earpiece. "Ready when you are," she whispered. After his reply, she pulled the chair over to the computer. Removing a disk from a drawer, she placed it into the machine an entered a set of keystrokes. "Let's put the blinders on," she thought aloud, making the final presses. As the machine executed its command, she walked out of the office and back to the bridge, awaiting whatever they had planned…<p>

* * *

><p>Inside of his office, Commander Ikari took a call. "I see…" he said into the phone. "No, there is no concern…continue watch." Placing the device back in its place, he turned to the others in the room. "It seems video is down around headquarters," he said. "Technical error."<p>

"It is him," Kaworu Nagisa said.

"Of course," Gendo replied. "I knew he would be back."

"Should I go?" Rei asked.

"No," Gendo answered. "I'll need you nearby if we are to start it."

"Then it is time?" Rei asked.

"Soon, it seems," Gendo replied. Turning towards Kaworu, he spoke. "Find and stop him. But do not kill him."

"I shall stop just short, then," Kaworu said, turning and leaving the room.

As the Fifth Child went out of earshot, Rei spoke up. "You do not trust him."

"He worked for the Committee," Gendo said. "I have all the reason I need to watch him closely." He turned his chair around to look out the window. "Follow him, Rei. Eliminate him if he deviates even slightly," he ordered.

"Yes sir," Rei said with a bow before exiting the office herself.

The Commander could only smile as the pieces began to come together for his scenario…

* * *

><p>The four intruders exited into the Geofront, the elevator trip long and silent. Stepping out into the underground area, they made a beeline for the entrance to the NERV pyramid. After some time, they made it into the hallways inside. But there, they began to find security officers dead, their necks snapped by great force.<p>

"There's someone else besides us here…" Misato said, her eyes darting between hallways. "Everyone watch your backs."

"You think it was Rei?" Shinji asked.

"Not sure…" Kaji said, looking at the injuries. "This wasn't quick and clean, whoever did this wanted pain."

"Okay, bridge is this way. That's where they'll be waiting," Misato said, motioning down one of the halls.

Readying their weapons, they began to head down that way…until Asuka noticed Shinji had stopped in his tracks. "What are you waiting for?" she asked.

Shaking his head, Shinji looked back at the three of them. "No, I'm going the other way."

Asuka shot him a puzzled look. "But that way goes to the cages. Why-"

"That's where he'll be," Shinji said in a quiet voice. "I just know it."

Misato looked on with a pained expression. "Are you sure?"

"Yeah," Shinji said. "You guys go ahead and get to the others. You know what I've got to take care of…"

"Sometimes, a man's gotta bury his own demons," Kaji said to Misato.

Asuka turned to Misato and Kaji. "You guys go ahead, I'll catch up." Nodding, the two of them continued down the hall. The redhead then turned back towards the boy. Hanging her head to hide her face, she quickly grabbed Shinji by the collar and pinned him against the nearby wall.

"What the hell?" Shinji said with a start.

Asuka looked up at him with eyes full of anger and worry. "You listen to me and you listen good," she said, her voice cracking. "You'd better make it back, alive and in one piece, or I swear…I'll hunt you down and kill you myself!"

Shinji smiled, pulling the girl into a tight hug. "I promise…" Releasing her, he quickly pressed his lips to hers and held them there for a few seconds. "For luck, okay?" he said, the faintest hint of tears in his eyes.

Asuka nodded, holding in her own tears. "Sure thing," she replied, running silently down the hall to catch up to Misato and Kaji.

Taking a long and deep breath, Shinji began his leisurely walk down another hall, the gun in his hand darting around the corridor. "Come on, father," he said to himself, "let's finish this."

* * *

><p>The other three had crept down several similar hallways, finding more dead security officers and noticing the lack of any noise or activity. Opening the door to the bridge, they were met by the sight of Ritsuko Akagi and the rest of the bridge crew. "Good, you've made it," she said.<p>

"You alright?" Misato asked her old friend.

"About as good as you'd expect," Ritsuko replied. "Why? What's happened?"

"Somebody's already here," Kaji answered. "All the way from the entrance, we've been finding dead security."

Ritsuko's expression hardened slightly. Walking over to one of the consoles, she typed away madly. On the screen, a video feed from one of the deeper parts of NERV was shown. "Bypassing my program a little to see what's happening," she explained.

The video feed showed a view of two security officers keeping watch over the area near Unit-01's cage. From down the hall, Kaworu approached. As he neared the men, he quickly took hold of one man's neck and snapped it.

"The Commander was right not to trust him," Ritsuko mused.

Misato, Kaji, and Asuka just watched the scene unfold further. As the other man reacted, he fired on the Fifth Child. But the bullets were stopped by a familiar shape forming around him. "Oh my God…that's an AT field!" Misato shouted.

Ritsuko watched the footage with a horrified look. "No wonder the Committee placed him here…" she said. "Taking security offline did the same to the Angel alarm."

Asuka watched the footage again, her face a mask of terror. "Shinji…" she whispered.

"Well at least we know where the last one is now," Misato said, turning towards the crew. "How soon can Unit-01 be prepped?"

"It's been locked down in Bakelite," Makoto said. "We can still get things started, though."

"Shit!" Misato fumed. Pressing the earpiece, she hoped she could get ahold of Shinji before it was too late…

* * *

><p>Shinji had traveled down the myriad of hallways within headquarters, searching for his targets. As he neared the cage leading to Unit-02, Misato's voice came from his earpiece. "Shinji, come in!"<p>

"What is it?" Shinji answered, opening another door and finding another dead guard on the other side.

"We've just hit a bit of a serious problem," Misato said. "The Fifth…he's the final Angel!"

Shinji's eyes widened. "Are you sure?"

"Ritsuko hacked into the video feed and found him," Misato explained. "He's the one who's been killing security."

"Do I have time to get to Unit-01?" Shinji asked.

"Unit-01's still in lockdown. It's gonna take some time," Misato replied.

But Shinji had run out of time. As he rounded the next corner, he caught sight of Kaworu. The Fifth Child was dressed in that now-familiar black plug suit and a malicious grin on his face. "Ah, Shinji," he said in a soft voice. "I just knew it was you."

Shinji placed his handgun under his belt and raised the submachine gun in the other boy's direction. "And you're Nagisa," he said, trying to remain calm despite what was happening.

"Ah, then there are no introductions needed," Kaworu said. Noticing the gun pointed at him, he laughed a little. "I assure you, that will not work," he said. Shinji ignored him and fired a burst in the Angel's direction. As the rounds bounced harmlessly off the now-visible barrier, the boy dropped the gun in defeat. "I told you…a futile gesture," the Fifth Child continued.

Turning and running back down the hall he'd come from, Shinji rounded the corner and leaned back against the wall, trying to calm his breathing. 'Gotta make it back to the EVA cages,' he thought, going over the routes to there in his head. "Why not just get what you came to do over with?" he asked. "Why go through all the song-and-dance with the Commander and SEELE?"

"Ah, because it was fun," Kaworu said. "I quite enjoy how Lilim deceive and hurt one another."

"What?" Shinji asked, edging down the hall a little.

"The Committee saw fit to train me in all manner of ways to hurt and kill others," Kaworu explained, "and all the while, they knew of what I was. I can thank them for one thing, though."

"Oh yeah? What's that?" Shinji questioned.

"The enjoyment of human death," Kaworu said with an evil smile. "It is quite exhilarating…looking down at someone while the life drains from them."

"Are you insane?" Shinji asked.

"No…I just enjoy such things," Kaworu said. "Who do you think killed those guards?"

"Why did you do that?" Shinji asked. "They weren't even after you…"

"I became bored awaiting your arrival," Kaworu answered. "I had not killed since the Committee was undone. Besides, they would die after I was through with you, anyway."

"Th-that's…you're sick!" Shinji yelled.

"Be that as it may," Kaworu said with a shrug, "I did rather enjoy how the Commander set the Committee against themselves. Your father does very good work." Shinji didn't reply, only making a break for the door and back into the bowels of NERV, hoping to get back to Unit-01 and take care of the last Angel. "And now the chase is on," Kaworu said, his pace never increasing from a slow walk…

* * *

><p>"Is it ready yet?" Misato ordered. The bridge crew had worked double-time to prep the purple EVA to combat the 17th Angel.<p>

"Entry plug is partially inserted, but we can't free Unit-01," Maya answered. "Shinji's going to have to get it out of there."

Asuka watched the feed from the cage with a worried expression. "Shinji…just make it there, please."

* * *

><p>As Shinji ran through what felt like the thousandth hallway that night, he was at a loss to figure out how to finish things up. The final Angel was stalking him down the halls, never getting in a hurry to finish the job. A couple of more corners later, he found himself passing the pilots' locker rooms. 'Getting close,' he thought, following the hall to the end. Opening the door at the end, he was greeted by the sight of the machine he'd been seeking, the entry plug sticking out of its neck. "Made it, Misato," he said.<p>

"Okay, just get inside," Misato ordered. "You'll have to free it, though."

As Shinji began to climb the side of Unit-01's head to reach the plug, a sharp pain knocked him back down onto the catwalk. Looking over, he saw the glow of a familiar barrier around the Fifth Child.

"If you can use an AT field offensively, why not just finish me with it?" Shinji asked, gritting his teeth.

"Ah, but that would deprive me of the fun of the hunt," Kaworu said, slowly moving down the catwalk.

"You really are a sadist, you know?" Shinji joked, trying to find a way to Unit-01.

"The old men taught me very well," Kaworu said. "I don't want to make it quick for you," he explained, walking towards the Third Child in short steps, "you are the last thing between me and returning to Adam, what with the Second unable to use Unit-02 and the First without Unit-00. And I intend to make good use of our time."

Shinji began to slowly edge away from the grey-haired boy, feeling that death was imminent.

"I am looking forward to crushing the last breath from you," Kaworu said, standing less than two feet away. Shinji closed his eyes in preparation of the end.

But this was not to be the case as more than two dozen bullets ripped through the Fifth Child's body. A look of horror on his face, Kaworu dropped to his knees and pouring blood from the many wounds in his body. "W-what?" he choked out, spitting up more red liquid.

Shinji looked past him to see Rei, dressed in the black plug suit and holding the submachine gun he'd dropped in the hallway. "Rei…" he spoke, feeling more glad to be alive than he ever had.

"I am glad I made it in time," Rei said, dropping the empty gun.

"Ha…I knew y…you couldn't be trusted," Kaworu managed.

"Be slient," Rei said, getting the Fifth Child to his feet. "The same could be said of you, Nagisa."

"W…what are you-" his words were cut off and replaced with pained screams as Rei plunged a hand through his wounds and into his torso.

Shinji silently watched the spectacle, feeling sick to his stomach.

Rei ignored the screaming and reached deeper into his body, finally finding what she was after. Placing a foot on his back, she pushed it in while pulling her arm out. With one solid jerk, she loosened a faintly glowing red orb from his form.

"Th…that's…" Shinji tried to form the words.

"Correct," Rei said, "his core. He will not last long separated from it."

Looking down, Shinji could see the life drain from the last Angel. As it did, the core stopped giving off its faint glow. "Then it's over?" he asked.

"No," Rei said, tossing the dead core down. "There is still Commander Ikari. Shall I call him down here?"

"Not just yet," Shinji answered. Reaching for his earpiece, he spoke. "Misato, Nagisa's dead."

"Yeah, we…can see that," Misato's voice said. "Remind me not to shake Rei's hand anytime soon."

Shinji shook his head at her choosing a time for joking. "That's just terrible…"

"Well, you saw it happen…" Misato shot back.

"Misato…take everyone and get out of here," Shinji said in a more serious tone.

"Are you sure?" Misato asked.

"It's only father left," Shinji answered. "I can take care of this from here. Just get them out of here."

"You're certain?" Kaji's voice questioned.

"I…I don't know," Shinji said. "But whatever happens, I'm not going along with his plan."

"What are you talking about, idiot?" Asuka's voice came in.

"Just what I said: he won't take me alive…" Shinji said in a quiet tone. He then turned to Rei. "Alright, do it."

Rei nodded, taking a cell phone out of a pocket on her leg and dialing the Commander's office. "I have him," she said. There was a pause as she listened on the other end. "Understood," she replied, hanging up. "Get on your feet," she told Shinji, upholstering her own handgun and pointing it at him. "Are you armed?"

Shinji nodded, removing the weapon from his belt and held it by his side, ready for the final performance…

* * *

><p>Misato's face didn't betray how she felt internally. She knew well what Shinji had meant. "Okay…" she admitted. "You just take care of yourself."<p>

"You're not really gonna leave him here, are you?" Asuka yelled at the major.

Misato looked at the redhead with her most serious expression. "Asuka…" she began, "I trust him to take care of it."

Kaji placed a hand on the young girl's shoulder. "Have faith in him," he told her. "He's going to make it."

"He'd better," Asuka said under her breath.

Misato then turned towards the last few NERV employees. "Alright, everyone follow us."

The seven of them worked their way back to the entrance of NERV headquarters and out into the Geofront. As they approached the elevator, Misato turned back towards the pyramid. "Shinji…be careful," she whispered before boarding…

* * *

><p>Back in the EVA cage, the First and Third Children remained in the positions they were in. Her pointing a gun at him, and him awaiting the Commander.<p>

"Shinji…" Gendo's voice came from behind Rei.

Shinji raised the weapon in the man's direction, no waver in his hand. "Father…" he said though clenched teeth.

Looking down at Kaworu's body, Gendo smiled coldly. "It seems the Committee had left a Trojan Horse of sorts as their last act of desperation," he said, turning to Rei. "Very good work."

"Yes sir," Rei said, her gun trained on Shinji.

"Enough of this nonsense," Shinji said. "I will not go along with your insane scenario."

"And what do you know of it?" Gendo asked his son.

"I know just what you're after," Shinji answered. "Mother's still inside this damned thing…" he said, referring to Unit-01.

Gendo was not taken aback in the least. "So you knew…"

"Since it absorbed me," Shinji answered, "but then I was told of what you were planning…"

"Ah yes, the Second had failed to eliminate Major Katsuragi," Gendo said.

"I will not do it," Shinji repeated, releasing the safety on his gun.

"I did not say you had a choice," Gendo said, removing his own weapon from his coat. "The only choice you have is whether it will be willing or not."

"I have made my choice," Shinji said, his voice low and angry.

"Very well then," Gendo said. "Rei."

Nodding, Rei took the safety off her own weapon…and pointed it at the Commander's head. "Drop your weapon. Now."

Gendo couldn't hide the surprise on his face. "What is this?" he asked angrily.

"This is your chance to surrender," Shinji replied. "I'd take it."

Ignoring him, Gendo stared at Rei. "You have been helping them…how dare you do this to me, I raised you-"

"…to be a weapon," Rei interrupted, "a tool for your plans. I am done."

"Why?" Gendo asked, feeling his scenario fall apart.

"I am…tired," Rei spoke in a quiet voice, small tears falling. "Tired of killing, tired of being used. I wish to be free of this…"

"Rei…" Shinji said softly.

Gendo closed his eyes and calmed himself. There was still time to put this back on track. "If that is what you wish…"

Shinji saw the slight turning of his gun towards her. Acting fast, he quickly shot the arm holding the gun. The Commander grunted in pain, dropping the weapon. Another shot after that hit his leg, causing him to drop to his knees. The boy walked over and placed the gun against the man's head while sliding the dropped weapon away with his foot. "Move again and I'll take my time," he said in a voice like his father's.

"Ikari…" Rei spoke quietly, lowering her weapon and dropping it.

"Rei, get out of here," Shinji said, his voice normal.

"What are you going to do?" Rei asked. Silence hung in the room, the answer already known to all. "You are going to kill him."

"Yes," Shinji replied quietly.

"Why?" Rei asked.

"Because we'll never be free," Shinji explained. "As long as he's alive, you or I or Asuka will always be looking over one shoulder…wondering if he's going to come for us."

"Are you certain of this?" Rei questioned.

"I wish there was another way…" Shinji answered. "But this is how it must be."

Rei remained silent, looking down at the man who had raised her. She felt sadness at what was to happen to him, but also anger at being used for his plans. But if it was necessary to be free…

"Help me, Rei," Gendo spoke up.

Rei considered his words for a second. "No," she said, walking to the door and leaving the room.

As the door closed, Gendo spoke up. "You won't kill me."

"Keep telling yourself that, father," Shinji replied, pushing the barrel closer to him.

A long tense silence fell across the room for several minutes. "Then why do you hesitate?" Gendo asked, laughing a bit. "Are you waiting for some kind of confession, something redeeming I could say and absolve me?"

"No," Shinji answered. "There is nothing you can say that will redeem you. I'm thinking of what the last thing I will say to you will be."

"And what is it, then?" Gendo asked, feeling light-headed from the blood loss.

Shinji stood in silence as he contemplated what they would be. So much to say, so much hate for this man. But there was one thing above all of it. Something he had to say. Closing his eyes, a few tears fell as he found the words. "I forgive you." Gendo turned his head to look at Shinji, who lowered the weapon and placed it under his belt. "Even after everything…I can't do it. You should pay for what you've done. But not by death…"

As his son walked away, Gendo reached over for his own weapon with his unhurt arm. "Get…get back over here," he said through clenched teeth. "You can't take everything apart and just walk away from me." Pointing the gun at him, he concluded, "You're still a coward."

Shinji turned around to face the Commander, his face blank. "No," he spoke up, "I'm just not as willing to discard everything as you are."

As Gendo's finger moved to the trigger, an unearthly roar erupted from the once-silent machine nearby. Seconds later, a huge purple hand dislodged itself from the Bakelite and came down on the walkway, giving the structure and the Commander a death-grip.

Shinji, having been knocked off his feet, stood back up and looked at the scene. Unit-01's hand now covered most of the walkway, blood running between its fingers. "Mother…" Shinji said softly, closing his eyes. Walking over to the hand, he spoke up. "I meant it, you know," he said, "I do forgive you." He then moved towards the head of Unit-01. "I'm sorry, mother. But you know it had to be this way." He ran a hand over the cold metal of the machine. "Goodbye…" he said softly. Walking away, he looked back at the sight behind him. Blood and death, the only way it could've ended…

* * *

><p>Back outside, Shinji decided to sit near the lake created by Unit-00's destruction. He then removed the gun from under his belt and tossed it into the water. His thoughts were a mess, but he felt no anger anymore. "Is it done?" a soft voice shook him from those thoughts.<p>

Opening his eyes, Shinji saw Rei standing near him, dressed in her standard school uniform. "You heard it, too?" he asked sadly, wiping fresh tears away.

"Yes," Rei said. "But it was not something you could have prevented. It was her will, not yours."

"I know," Shinji admitted. "And we know it had to be done. But still…"

"It will weigh on you forever, will it not?" Rei asked, feeling some sadness herself.

Shinji nodded, feeling the tears come again. "I'll just have to live with it…" he said with a cracking voice. As he began to cry again, he felt arms wrap around him. Opening his eyes, he saw Rei holding him. "Rei…"

"I am not practiced in consoling others, but…I will do what I can to help for now," the First Child said, small tears of her own forming. Shinji returned the hug, crying into her shoulder.

His tears under contol again, Shinji released the girl. "Thank you, Rei. You're a true friend."

The same smile he'd seen after the 5th Angel crossed her face. "You are welcome," she said, standing up to leave. "Where will I go? I have only known this place…"

"It doesn't matter," Shinji told her, shaking his head, "just get out there and…live. That's what I'm going to do."

Walking away, Rei turned back towards him. "Will we meet again?"

Shinji smiled widely. "It's a wide world out there," he said, mirroring Mathieu's words, "you just never know."

Rei nodded, the smile leaving her. "Goodbye…Shinji."

By himself again, Shinji settled into the quiet of his thoughts for almost three hours, watching the sun rise. He knew he'd have to live with what happened that night. But to trade some personal sanity for the fate of the world? That was a fair enough tradeoff for him. Getting to his feet, he walked back out into the forest. He figured he's stay out there for a few days, needing a little time alone for now…

*****One week later*****

"It's such a beautiful day…" Asuka's musings were certainly accurate. Osaka was a much more active and lively place than Tokyo-3 was. She had arrived a few days ago, needing a break from the bunker's stale atmosphere. Staring at the clouds, she felt genuinely at peace. Well, almost.

Shinji's fate was still unknown to them. All they knew was that all had been quiet from NERV, so that was a good sign. But the internal storm within Asuka had not quelled even slightly. That night they had been together…she smiled at just how strong yet gentle he had been with her. 'Idiot,' she thought, none of the usual tone behind the insult. 'I want to see you again.'

Sighing, Asuka resumed her walk down the busy street. She was dressed in a red bikini, a slightly see-though skirt and shirt covering her and a pair of sandals on her feet. The most striking thing, however, was her change of hair color. Misato suggested that the Second Child hide her identity until they knew Shinji was alright, and neither felt that it was a bad idea. The major had offered that she dye it, something the redhead was vehemently against. So she had chosen a brunette wig, long enough to cover her fiery locks. Her eyebrows were dyed to match, a pair of brown contacts to complete the look. Sure, her features didn't exactly look Japanese, but it would take someone studying her closely to realize that. That, or someone that knew her.

Walking past a vendor selling sunglasses, Asuka tried several pairs on. 'None of these really complete the look,' she mused, searching through the options. Picking up a sleek black pair, she decided these were the best she would find. After paying for them, she resumed her walk again.

Another five minutes of travel later, Asuka stood in front of a fountain near the center of town. She stared into the clear water, her reflection looking back. She smiled a sad smile, her thoughts returning to her roommate. "I hope you're okay, Shinji…wherever you are."

"Hello? Can you help me? I'm looking for someone," a voice came from behind the former Second Child.

"And what makes you think I can help?" Asuka asked back, not turning around. She had been talked to by a lot of guys using this approach already. 'Just another one on the pile,' she thought.

"Because you look a lot like her…" the voice said.

Asuka's eyes widened as she recognized the voice. Spinning around, she came face-to-face with Shinji Ikari. He was dressed in khaki shorts and a blue t-shirt, his feet in sneakers. Her mouth suddenly found itself unable to form the words, her eyes wanting to water. "Hey there," he said in a casual tone, his smile wide and arms open.

"Shinji…" was all Asuka could manage before she stepped into the embrace. The two held onto each other tightly, both tearing a little. "You kept your promise," she said, resting her chin on his left shoulder.

"Of course I did," Shinji said, leaning against her. "I just needed to be alone for a while. Had a lot to think about, you know?"

"But you still suck for being gone like that," Asuka whispered in his ear, teasing him.

"I'll make it up to you," Shinji told her, his face turning slightly red. "I'm not going anywhere."

"Good to know," Asuka said, releasing him a small bit, but not fully. "I hope you brought a present, though," she said in her usual attitude. "It'll be a start on 'making it up'."

Shinji gave her a nervous smile. "There is this one thing…" he offered.

"Oh? What's that?" Asuka asked. Her question was immediately answered as Shinji wrapped his arms around her again and kissed her deeply, his tongue just barely in her mouth. The girl shivered slightly, the sensation making her a bit dizzy. She returned the affection as best as she could. The two of them stood by the fountain in that position for what felt like hours until he pulled away slightly, blushing and smiling brightly.

"That answer your question?" Shinji asked, thoughts still a little hazy and his breathing heavy.

"Very…much…so," Asuka said, leaning against him. "I'd like presents like that more often," she told him after catching her breath.

"As much as you want, Asuka," Shinji said, kissing her forehead. "You have me for as long as you want."

Asuka gave him her purest smile, a look of contentment she rarely showed. "Idiot…" she said sweetly. "But just as long as you're my idiot…"

"So what would you like to do today?" Shinji asked after a long silence.

Letting him go, Asuka kept hold on one of his hands. "Wherever's fine with me. Didn't have anything to do, anyway."

"Yeah, that sounds good," Shinji agreed.

The two teens began to walk back into the busy city, ready to begin a much quieter life than they had left behind…

*******To be continued…*******

**A/N:** Oh my, that was kind of a sad and violent chapter…with a nice, light finish. Odd combo, I know. But if you know me well enough, it's oddly fitting.

Yeah, I gave Rei a chance to be in some touching scenes and kick some serious ass in this fic. Someone once said I underutilized her. They can't accuse me of that this time…

And now, only the epilogue left to go. It's more like the ending to this part, so stick around if you're a fan of 'em.

And sorry to any Kaworu fans, I just figured I could tweak him into something darker. Besides, you know I'm part of your demographic, anyway (see Nephilim, for example).

*******Omake time!*******

The camera pans into the familiar room, the author putting the final few touches on this chapter.

Bard: (to himself) Three down…almost done. (notices the camera) Oh, hi there. Back again, are we?

Mitsumi suddenly pops out from thin air into the room.

Mitsumi: (grinning) Hiya!

Bard: (wide-eyed) Wha-…when did you learn how to do that?

Mitsumi: Oh…a while back, while you were on hiatus.

Bard: (sighing) That figures…

Mitsumi: Next one's done?

Bard: Indeed it is. Would you like to look over it?

Mitsumi: You DO need someone to pick it apart…

Bard: (nonplussed) Oh really?

Ignoring him, Mitsumi takes a seat on the author's shoulder and looks closely over the above chapter.

Mitsumi: (some time later) I see where you fit in the last one's end…and it ends on such a sweet note. A little violent in spots, though.

Bard: Necessary evil, my dear. Just as the sex was.

Mitsumi: I only have one real quibble, though… (begins crying) WHY'D YOU HAVE TO KILL KAWORU-KUN?

Bard: (surprised) Eh? Never pegged you for a fan…

Mitsumi: (grabbing his collar and shaking his head back and forth) I ALWAYS HAVE BEEN, BAKA!

Bard: (shaken and dizzy) Uh…my bad?

Mitsumi: (calmed down but glaring) Not gonna work, mister!

Bard: Okay, okay…how about to make up for it, I'll perform with the others next chapter?

Mitsumi: (releasing him and smiling) That'll work for me, baka-author.

And with that, Mitsumi disappears again.

Bard: (sighing) Oh dear… (looking at the camera) Time for you to be going, I think.

*******End Omake*******

Pre-read for this chapter was again done by the team of Dark Machine, Eric Blair, gesser87, and JimmyWolk. Good work as always, gentlemen.

Small note: this chapter and all previous/following it were written around late June/early July last year. So a quick "sorry" to everyone who may have been waiting for something after TLaWR. Revisions and pre-reading can take quite a bit of time, it would seem…

For any of you who are new to the community, all of my older (2004-2006) works have undergone a small bit of tweaking (as of the 14th of June 2010). So go take a look, tell me what you think. And review! Even if it's not positive, review!

As usual: good comments will be appreciated, bad ones will be ignored (or kept for firewood). But I do favor good/helpful criticism, so send it my way!

**-AngelNo13Bardiel-**


	4. From the Edge of the Deep Green Sea

See Chapter 1 for disclaimer.

**THE IKARI IDENTITY**

Chapter 4: From the Edge of the Deep Green Sea

* * *

><p>Somewhere near Osaka, two people slumbered soundly in a small house. Shinji opened his eyes in the first morning light, sitting up in bed. Taking a quick look over at Asuka's sleeping form, he quietly rose from the bed and walked out the front door and onto the beach. It was a quaint place that they'd stumbled upon a few weeks back and decided to stay for a while.<p>

Taking a deep breath of the morning air, Shinji felt a small measure of peace. It had been a little over a month since that night, and it still hung over him like minute one. But it wasn't like he didn't have help with that. Staying with Asuka here for a few days after their reunion, they had returned to the bunker to show that he was alive and well. Misato and Kaji had been relieved, her more so than him.

'I'm glad they believed in me,' Shinji thought. The bridge crew had stayed around for a week before quietly going their own ways, just glad their time with NERV was over. Ritsuko had opted to stay, saying she needed to make up for lost time with her old friends. All had been quiet around headquarters since, but he hadn't really paid attention. He was just glad it was over…

Walking back to the structure, Shinji sat down at the foot of the stairs, watching the sunrise. He and Asuka had decided to leave the bunker for a while, just needing some time away from the past. Kaji had stashed away quite a bit of what both the Committee and the Commander had paid him. The house wasn't very expensive, so they could afford to stay here for a long time if they wanted to. It was a bit smaller than Misato's old apartment, but it was enough to get by.

Shinji's thoughts returned to the girl he was living with. Asuka had grown more comfortable around him, and they had settled into a mutual need for one another. He wasn't really sure what they were, only that neither were going anywhere without the other. He had told her how he felt, but she was still contemplating her own words. 'I said I'd give her all the time she needed,' he thought with a smile. Since that night, they hadn't been…intimate again, but it wasn't really necessary. They had all the time for that one day ahead.

And, surprisingly, they had both resumed training with their skills. Not like that one night's out-of-control sparring match, these were much more leisurely. Neither let the other take the upper hand or get too into it. It was more of a dance to them, something that brought them back to that moment. Of course, Asuka was usually the winner of most of these…her aggressive nature being key to that. But Shinji was just glad because of the bonding experience it gave them. 'And if I should ever need to protect myself or her,' he thought. The last part made him laugh a bit, the idea that the redhead needing protection almost comical.

Shinji then recalled the nightmares. They'd both get them often, him more often than her. His mostly concerned the last images of his father. Asuka's were much harder to shake off, the ones about her mother's death and the 15th Angel's attack at the forefront. It was how they ended up most nights, one would awaken and the other would hold them until they went back to sleep.

A pair of slender arms wrapping around Shinji's neck shook the thoughts from him. "Morning," Asuka purred in his ear.

Shinji smiled and turned his head, giving her a quick kiss. "Beautiful…" he said, not really sure if he meant her or the morning.

"Don't be corny," Asuka teased. Sitting beside him, she watched the sun slowly creep into the sky. "Penny for your thoughts?"

"Just thinking about everything," Shinji answered. "But not really thinking about anything, either."

"Geez, be a little more cryptic, why don't you?" Asuka complained, giving him a small push.

"Sorry…" Shinji said with a smile.

"Don't fall into old habits," Asuka said, her tone playful. "Still feeling down?"

Shinji sighed. "I'll always feel this…"

Asuka placed her hand over his. "I know…I don't think we'll ever forget those times. We can just try and overwhelm them with better times."

"I'm glad you're here with me," Shinji said.

"Just so long as you're there for me," Asuka replied.

"I told you before," Shinji said, looking at her, "as long as you'll have me."

Asuka sat quietly with him, her attention returning to the sky. "I really love it here," she said after a long silence.

"Yeah, it's like a little piece of Heaven," Shinji agreed.

Asuka leaned her head against him. "Cause I'm here?" she asked.

Shinji nodded. "Yeah…"

Asuka gave him a small smile before kissing him lightly. "Listen, I know you told me before. But…"

"But?" Shinji questioned.

"Tell me again," Asuka requested. "I need to hear it."

Shinji knew just what she meant. Pulling her into a hug, he whispered in her ear. "I love you."

Asuka felt a single tear fall. She hugged him back tightly. "Thank you." Her expression lowered a little. "I know I haven't-"

Shinji cut her off by placing a finger over her lips. "You don't have to say it," he said, lowering the digit, "I can tell."

Asuka leaned in and kissed him again, holding this one longer. As they parted, she spoke up. "We can't do this all day, we need to go into town."

"Yeah, need some groceries," Shinji agreed. Getting to his feet, he extended a hand to the girl. Asuka took his hand and rose from the steps. The two of them walked back into the house.

* * *

><p>After having showered and dressed for the day, the couple found themselves walking into Osaka. Shinji was dressed in a blue t-shirt and white shorts, Asuka in her familiar yellow sundress. "It almost feels like a honeymoon," she mused, looking at the clouds.<p>

"Except we're not married," Shinji answered.

"That doesn't mean it can't feel like it," Asuka replied. "And that doesn't mean we can't one day…" she said quietly.

"R-really?" Shinji asked, feeling a little blush creeping up.

"Nope," Asuka said with a smirk, sticking out a bit of tongue. "At least, not yet. Still too young."

"I certainly don't feel young…" Shinji said sadly.

"It is what it is," Asuka said in a philosophical manner. "We can try make up for all that lost innocence, though." Looking over at him, she continued. "Right?"

"Yeah…I'd like that," Shinji said, taking hold of her hand.

They walked in silence for a little while longer. "When do you think we should go see them again?" Asuka questioned.

"Sometime soon," Shinji offered. "They're probably wondering why they haven't heard from us."

"Yeah, it has been more than a week since I called…" Asuka said.

"Maybe we should do that while we're out," Shinji said.

"Sure," Asuka answered. The rest of the walk was silent, the both of them enjoying the peace of the day.

* * *

><p>The two returned to the small house just as evening arrived. They had walked all around Osaka and the beaches nearby, just taking in the sights. It had probably been the tenth-or-so time they had, but it was still just as nice. 'So different than either Tokyo,' Shinji had thought earlier. It was certainly less gray and imposing.<p>

Setting the groceries they'd bought on the counter, Shinji began to prepare something for dinner. Asuka took a seat at the small table, stretching her arms and legs. "That was a nice long walk," she said. "What's on the menu?"

"Vegetable stir-fry," Shinji answered, turning the stove top on.

"Sounds good," Asuka replied.

They let the quiet hang in the room as he continued cooking, both just enjoying how things were going. After the meal was finished and eaten, they went outside and laid down at the edge of the sea. The night was just beginning to set in, the sky bathed in twilight.

"Hey Shinji," Asuka said, laying with her head on his right side.

"What?" Shinji asked, staring into the sky.

"Tell me what you're thinking," Asuka requested. "I know something's bothering you."

"Well," Shinji began, "I miss Rei." He stopped here to choose his words carefully. "It's just…she's one of the best friends I've had. If it weren't for her…I don't know. I think you'd be gone and I'd still be my father's puppet. I may have finished things, but she's the real hero here."

Asuka nodded. "I never really thanked her properly, either," she said sadly. "Think we'll see her again?"

Shinji shook his head. "I don't know…I hope so."

Asuka laid her head back down on his body, listening to his heartbeat. "Shinji…thank you."

Shinji smiled down at her. "You don't need to do that."

"No, I really mean that in every sense," Asuka said, her eyes meeting his. "I've never felt so calm. I wouldn't know what to do if you weren't here when the nightmares come…"

Shinji hugged her tighter. "I understand. You're doing the same for me."

Asuka leaned in closer to his face, their lips nearly touching. Just a bit closer…

And that thought was cut off as the tide came in and soaked both of their backsides.

"Ah! Shit! Cold!" Asuka shouted while leaping to her feet, dusting sand off her dress and wringing out some of the salt water. Shinji couldn't help but laugh at the moment. Noticing his reaction, she became slightly irritated. "What the hell's so funny?"

"S-sorry, it's just…" Shinji managed between laughs, "that was pretty funny, huh?"

Asuka pushed him back down into the mix of sand and surf. Straddling his chest, she leaned down close to him with a wicked smile on her face. "Hey, idiot," she said, the insult almost a purr.

Shinji turned a bright red at that. "Y-yes?"

"I'm bored…" Asuka said sweetly.

Shinji's eyes widened greatly at the memory those words triggered. His train of thought was quickly derailed as Asuka pressed her lips against his urgently. Lips slightly apart, she shoved her tongue in his mouth. The boy's mind went blank for a few seconds before he melted into it. He mirrored her actions as best as he could, rational thought all but abandoned. Parting, he felt the tide ebb and flow beneath him, soaking him to the bone.

"That time was much more serious, huh?" Asuka asked, her breathing returning to normal.

Shinji could only nod dumbly, his mind in a fog. Had anyone told him six months ago where his life was headed, he'd have probably laughed himself to death. Now, though…

"Come on, it's getting late," Asuka said, her voice far away. Blinking a few times, Shinji realized that she had gotten off him and walked back over to the door. Shaking his head, he picked himself up off the beach and headed inside.

As the front door closed, a pair of eyes watched his and Asuka's every move from a hill some distance away. "Targets located," the figure spoke into an earpiece, the moonlight shining off a lens attached to a rifle…

*****To be continued in **THE IKARI SUPREMACY*******

**A/N:** Nope, we're not finished yet! This is just the end of the **IDENTITY** arc of the story. Expect **SUPREMACY** to be up soon…and maybe more after that. Might just end up as a trilogy, y'know?

Thanks for at least sticking around to read this part of the story. Your attention is much appreciated.

*******Omake time!*******

The camera pans this time, not into the author's room, but to the room next door…where a small stage has been assembled. The author is currently lugging in the speakers, with Mitsumi standing nearby talking to two of her sisters.

Magdalena: Oh, that's such a pretty dress, Mistumi!

Akari: I wish I had a guy who'd buy me such things…

Mitsumi: (smirking) Heh…it's not so much he bought it for me as much as I talked him out of it.

Akari: (grinning) Sneaky.

Bard: (turning towards them) Okay, stage is set. (looks to the camera) Oh, good timing!

The others take notice of the audience, Magdalena and Akari smiling and waving.

Magdalena: (shyly) Ah…so nice to see you again.

Akari: (turning to the others) Okay, everybody take your places.

As the fairies picked up their instruments (guitar for Mitsumi, bass for Magdalena, Akari seated behind the drums), the author walks up to the mic.

Bard: (sighing) The things I get talked into…

Akari gives a quick "one-two, one-two-three-four" count-off before making two sharp beats. A creepy but urgent bassline begins playing, drums entering at two more short intervals before becoming a steady beat. The guitar cuts in shortly after, a quick set of screechy chords repeating several times before becoming a steady riff with the rest of the music.

Bard: (singing)_  
>Sinister echoes clutching at straws<br>Letter boxes screaming  
>You try to pin him to the wall<br>You end up on the ceiling  
>Locked in a dome<br>The shadows flicker by  
>He's the madcap pusher<br>Delirium, the drug he's dealing_

_He drops a capsule in your drink  
>And spikes your dreams with madness<em>

_He's a sniper in the hills  
>Hiding in the holes in your head<br>He's the poison in your poison  
>The razor in your bed<br>Hanging on a picture  
>Eyelids' needle and thread<br>You empty yourself once again  
>But he's always one step ahead<br>He whispers in your ear  
>"Was it nothing that you said?"<br>He's walking in your sleep now  
>He keeps your fat paranoia well-fed<em>

_He drops a capsule in your drink  
>And spikes your dreams with madness<em>

_The sanity assassin  
>Assassin<br>Assassin  
>Stays up all night stalking<br>The sanity assassin  
>Assassin<br>Assassin  
>Picks off victims like flies<br>The sanity assassin  
>Assassin<br>Assassin  
>Let his fingers do the walking<br>The sanity assassin  
>Assassin<br>Assassin  
>The crack shot between your eyes<em>

_He drops a capsule in your drink  
>And spikes your dreams with madness<em>

The music comes to an end at that, the four occupants of the room smiling at one another,

Bard: (clapping) Very nice, girls.

Mitsumi: (nervously laughing) Hey, you're not too bad yourself. Think anyone'll know it?

Bard: (shaking his head) Dunno. Would be fun, though…

Mitsumi: (turns to the camera and waves) Bye! Come back and visit us again soon!

Magdalena, Akari, and the author join in waving goodbye to the camera as it pans away…for now, at least.

*******End Omake*******

Pre-read for this chapter was again done by the team of Dark Machine, Eric Blair, gesser87, and JimmyWolk. Good work as always, gentlemen.

Small note: this chapter and all previous/following it were written around late June/early July last year. So a quick "sorry" to everyone who may have been waiting for something after TLaWR. Revisions and pre-reading can take quite a bit of time, it would seem…

For any of you who are new to the community, all of my older (2004-2006) works have undergone a small bit of tweaking (as of the 14th of June 2010). So go take a look, tell me what you think. And review! Even if it's not positive, review!

As usual: good comments will be appreciated, bad ones will be ignored (or kept for firewood). But I do favor good/helpful criticism, so send it my way!

Until our paths next cross,**  
>-AngelNo13Bardiel-<strong>


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